def write_trajectory(universe, filename):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
for ts in universe.trajectory:
w.write(ts)
w.close()
def write_trajectory(universe, filename):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
for ts in universe.trajectory:
w.write(ts)
w.close()
def write_trajectory(universe, filename, maximum_frames=0):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
frame_count = 0
for ts in universe.trajectory:
if(maximum_frames != 0 and frame_count == maximum_frames):
break
w.write(ts)
frame_count += 1
w.close()
TRJ_LIST.append(sys.argv[2 + i])
outtrj = "traj.xtc"
# create a writer instance for the output trajectory
print "Reading trajectory %s" % TRJ_LIST[0]
u = Universe(topol, TRJ_LIST[0])
w = Writer(outtrj, u.trajectory.numatoms)
FRAME = 0
for j in range(len(TRJ_LIST)):
if u.trajectory.dt == 0.0:
print "No time step information found in the trajectoy file."
DT = raw_input("Input a float number for the time step:")
u.trajectory.dt = float(DT)
else:
print "Time step %6.4f was found and will be used in the new trajectory." % u.trajectory.dt
for ts in u.trajectory:
FRAME = FRAME + 1
ts.time = (FRAME - 1) * u.trajectory.dt
w.write(ts)
if FRAME % 100 == 0:
echo("Converted frame %8d ,time %8.2f\r" %
(ts.frame, FRAME * u.trajectory.dt))
if j < len(TRJ_LIST) - 1:
print ""
print "Reading trajectory %s" % TRJ_LIST[j + 1]
u = Universe(topol, TRJ_LIST[j + 1])
w.close()
print "Writing the result file traj.xtc finished."
outtrj = "traj.xtc"
# create a writer instance for the output trajectory
print "Reading trajectory %s" %TRJ_LIST[0]
u = Universe(topol, TRJ_LIST[0])
w = Writer(outtrj, u.trajectory.numatoms)
FRAME=0
for j in range(len(TRJ_LIST)):
if u.trajectory.dt==0.0:
print "No time step information found in the trajectoy file."
DT=raw_input("Input a float number for the time step:")
u.trajectory.dt=float(DT)
else:
print "Time step %6.4f was found and will be used in the new trajectory." %u.trajectory.dt
for ts in u.trajectory:
FRAME=FRAME+1
ts.time=(FRAME-1)*u.trajectory.dt
w.write(ts)
if FRAME %100==0:
echo("Converted frame %8d ,time %8.2f\r" %(ts.frame,FRAME*u.trajectory.dt))
if j < len(TRJ_LIST)-1:
print ""
print "Reading trajectory %s" %TRJ_LIST[j+1]
u = Universe(topol, TRJ_LIST[j+1])
w.close()
print "Writing the result file traj.xtc finished."
Index[nst] = [n]
else:
print "Error: ", n, nst, N_str
ifile.close()
print 'number of clusters:', len(N_str)
N_str.sort()
N_str.reverse()
N_write = int(raw_input('How many clusters you want to look at (eg. 8): '))
universe = Universe(pdbfile, pdbfile)
writer = Writer(filename + '_.pdb', universe.atoms.numberOfAtoms())
k = 1
for each in N_str[:N_write]:
if k > N_write:
break
percent = float(each) * 100 / sum(N_str)
for i in Index[each]:
print 'Writing cluster #' + str(i).ljust(3),
universe.trajectory[i - 1]
protein = universe.atoms
writer.write(protein)
print '%3i %5.0f%% %6.2f%%' % (k, percent, percent)
k += 1
writer.close()
