args = cli.parse_args()
trajlistname = args.trajListFns
atom_indicesname = args.atomListFns
trajext = args.iext
File_TOP = args.topology
homedir = args.homedir
n_clusters = args.n_clusters
n_macro_states = args.n_macro_states
stride = args.stride
# ===========================================================================
# Reading Trajs from XTC files
print("stride:", stride)
trajreader = XTCReader(trajlistname,
atom_indicesname,
homedir,
trajext,
File_TOP,
nSubSample=stride)
trajs = trajreader.trajs
traj_len = trajreader.traj_len
np.savetxt("./traj_len.txt", traj_len, fmt="%d")
if os.path.isfile(
"./phi_angles.txt") and os.path.isfile("./psi_angles.txt") is True:
phi_angles = np.loadtxt("./phi_angles.txt", dtype=np.float32)
psi_angles = np.loadtxt("./psi_angles.txt", dtype=np.float32)
phi_psi = np.column_stack((phi_angles, psi_angles))
else:
phi_angles, psi_angles = trajreader.get_phipsi(trajs,
psi=[6, 8, 14, 16],
phi=[4, 6, 8, 14])
trajlistname = args.trajListFns
atom_indicesname = args.atomListFns
trajext = args.iext
File_TOP = args.topology
homedir = args.homedir
n_clusters = args.n_clusters
n_macro_states = args.n_macro_states
# ===========================================================================
# Reading phi angles and psi angles data from XTC files
if os.path.isfile("./phi_angles.txt") and os.path.isfile("./psi_angles.txt") is True:
phi_angles = np.loadtxt("./phi_angles.txt", dtype=np.float32)
psi_angles = np.loadtxt("./psi_angles.txt", dtype=np.float32)
phi_psi = np.column_stack((phi_angles, psi_angles))
else:
trajreader = XTCReader(trajlistname, atom_indicesname, homedir, trajext, File_TOP)
trajs = trajreader.trajs
traj_len = trajreader.traj_len
np.savetxt("./traj_len.txt", traj_len, fmt="%d")
phi_angles, psi_angles = trajreader.get_phipsi(trajs, psi=[6, 8, 14, 16], phi=[4, 6, 8, 14])
phi_psi = np.column_stack((phi_angles, psi_angles))
np.savetxt("./phi_angles.txt", phi_angles, fmt="%f")
np.savetxt("./psi_angles.txt", psi_angles, fmt="%f")
# ===========================================================================
# Reading split assignments and the length of each traj
assignments_dir = args.assignments
labels = np.loadtxt(assignments_dir, dtype=np.int32)
if os.path.isfile(args.traj_len) is True:
traj_len = np.loadtxt(args.traj_len, dtype=np.int32)
else:
default=None, type=int)
cli.add_argument('-l', '--alignment', default=False, type=bool)
args = cli.parse_args()
trajlistname = args.trajListFns
atom_indicesname = args.atomListFns
trajext = args.iext
File_TOP = args.topology
homedir = args.homedir
n_clusters = args.n_clusters
n_macro_states = args.n_macro_states
stride = args.stride
# ===========================================================================
# Reading Trajs from XTC files
print "stride:", stride
trajreader = XTCReader(trajlistname, atom_indicesname, homedir, trajext, File_TOP, nSubSample=stride)
trajs = trajreader.trajs
traj_len = trajreader.traj_len
np.savetxt("./traj_len.txt", traj_len, fmt="%d")
# ===========================================================================
## get phi psi angles for Alanine Dipeptide
#if os.path.isfile("./phi_angles.txt") and os.path.isfile("./psi_angles.txt") is True:
# phi_angles = np.loadtxt("./phi_angles.txt", dtype=np.float32)
# psi_angles = np.loadtxt("./psi_angles.txt", dtype=np.float32)
# phi_psi = np.column_stack((phi_angles, psi_angles))
#else:
# phi_angles, psi_angles = trajreader.get_phipsi(trajs, psi=[6, 8, 14, 16], phi=[4, 6, 8, 14])
# np.savetxt("./phi_angles.txt", phi_angles, fmt="%f")
# np.savetxt("./psi_angles.txt", psi_angles, fmt="%f")