def main():
args = parse_args()
system_file = files.JSONStructInpFile(args.system_filename)
traj_file = files.TxtTrajInpFile(args.traj_filename, system_file)
dists = config_process.calc_end_to_end_dists(traj_file)
np.savetxt(args.out_file, dists)
def main():
args = parse_args()
system_file = files.JSONStructInpFile(args.system_filename)
traj_file = files.TxtTrajInpFile(args.traj_filename, system_file)
ref_ext = args.ref_filename.split('.')[-1]
if ref_ext == 'json':
ref_file = files.JSONStructInpFile(args.ref_filename)
elif ref_ext == 'trj':
ref_file = files.TxtTrajInpFile(args.ref_filename, system_file)
ref_config = np.array(ref_file.chains(args.step))
ref_positions = config_process.center_on_origin(ref_config)
aligned_positions, rmsds = config_process.align_positions(
traj_file, ref_config)
np.savetxt(args.outfile, rmsds)
def main():
args = parse_args()
system_file = files.JSONStructInpFile(args.system_filename)
traj_file = files.TxtTrajInpFile(args.traj_filename, system_file)
rgs = config_process.calc_radius_of_gyration(traj_file)
np.savetxt(args.out_file, rgs)
def main():
args = parse_args()
sys_inp_file = files.JSONStructInpFile(args.sys_filename)
traj_file = files.TxtTrajInpFile(args.trj_filename, sys_inp_file)
chains = traj_file.get_chains(args.step)
sys_out_filename = '{}.json'.format(args.out_filebase)
sys_out_file = files.JSONStructOutFile(sys_out_filename, sys_inp_file)
sys_out_file.write(chains)
def main():
args = parse_args()
system_file = files.JSONStructInpFile(args.system_filename)
domain_pairs = parse_domain_pairs(args.domain_pairs)
fileformatter = construct_fileformatter()
all_conditions = construct_conditions(args, fileformatter, system_file)
inp_filebase = create_input_filepathbase(args)
sim_collections = outputs.create_sim_collections(inp_filebase,
all_conditions, args.reps)
for sim_collection in sim_collections:
for rep in sim_collection._reps:
ops = sim_collection.get_reps_data('ops', concatenate=False)
runs = len(ops[rep])
for run in range(runs):
run_filebase = sim_collection.get_filebase(run, rep)
trj_filename = '{}.trj'.format(run_filebase)
trj_file = files.TxtTrajInpFile(trj_filename, system_file)
ops = datatypes.OrderParams.from_file(run_filebase)
all_dists = [[] for i in range(len(domain_pairs))]
for i, step in enumerate(trj_file):
config = np.array(step[0]['positions'])
for j, domain_pair in enumerate(domain_pairs):
pos_i = config[domain_pair[0]]
pos_j = config[domain_pair[1]]
all_dists[j].append(
config_process.calc_dist(pos_i, pos_j))
for domain_pair, dists in zip(domain_pairs, all_dists):
dist_tag = 'dist-d{}-d{}'.format(domain_pair[0],
domain_pair[1])
if dist_tag in ops.tags:
ops[dist_tag] = dists
else:
ops.add_column(dist_tag, dists)
adj_tag = 'adj-d{}-d{}'.format(domain_pair[0],
domain_pair[1])
adj_sites = np.array(dists) == 1
if adj_tag in ops.tags:
ops[adj_tag] = adj_sites
else:
ops.add_column(adj_tag, adj_sites)
dist_sum = np.sum(all_dists, axis=0)
tag = 'dist-sum'
if tag in ops.tags:
ops[tag] = dist_sum
else:
ops.add_column(tag, dist_sum)
ops.to_file(run_filebase)
def main():
args = parse_args()
# random.seed(123450897)
traj_file = files.TxtTrajInpFile(args.sim_filebase + '.trj',
args.system_file)
bias_tags, wins = us_process.read_windows_file(args.win_file)
bias_functions = json.load(open(args.bias_functions_filename))
op_tags = us_process.get_op_tags_from_bias_functions(
bias_functions, bias_tags)
ops = datatypes.OrderParams.from_file(args.sim_filebase)
op_to_config = sort_by_ops(ops, op_tags)
for i, win in enumerate(wins):
config = us_process.select_config_by_op_in_win(i, win, ops,
op_to_config)
win_filename = us_process.create_win_filename(win, args.out_filebase,
args.ext)
config_file = files.TxtTrajOutFile(win_filename)
config_file.write_config(traj_file.get_chains(config), 0)