from MMTK import *
from MMTK.Proteins import Protein
from MMTK.PDB import PDBConfiguration
from MMTK.Trajectory import Trajectory, TrajectoryOutput
from MMTK.DCD import DCDReader
import numpy
import math
import os
import glob


universe = InfiniteUniverse()

dirs = ['/net/gulrotkake/slars/groel_md/1XCK/116_1XCK_apo/results/traj_trimer/MMTK_50ns_noWAT_500frames_noATP_fitted_chain_*.dcd', '/net/gulrotkake/slars/groel_md/1XCK/129_1XCK_MGATP/results/traj_trimer/MMTK_*.dcd' ]

conf = PDBConfiguration('1XCK_chainALM_noWAT_noH.pdb')
chains = conf.createPeptideChains(model='no_hydrogens')
universe.addObject(Protein(chains))

i=0
files = glob.glob(dirs[i])
print files

# Create the trajectory object for output.
t = Trajectory(universe, "trimertraj_%s.nc" % str(i), "w", "Converted from DCD")

#for j in range(0,2):
for f in files:
    #f = files[j]
    print f
    dcd_reader = DCDReader(universe, dcd_file = f,
                           actions = [TrajectoryOutput(t, "all", 0, None, 1)])
    # Run the reader...
    dcd_reader()

# ... and close the output trajectory.
t.close()