def load_trajectories(conn, ss_id, param_dict):
e_id = execute_query(conn,
"""select expjobs_insert({0}, Null, Null, Null, Null, Null)""".format(ss_id))
trj_list_fn = os.path.join(param_dict['trj_dir'], param_dict['trj_list_fn'])
pdb_fn = os.path.join(param_dict['pdb_dir'], param_dict['pdb_fn'])
with open(trj_list_fn, 'r') as ifp:
fn_list = ifp.readlines()
fn_list = map(lambda t: t.split(',')[1].rstrip(), fn_list)
for dcd_fn in fn_list:
trj_id = execute_query(conn,
"""select trajectories_insert({0}, Null, Null, Null, Null)""".format(e_id))
trj_fn = os.path.join(param_dict['trj_dir'], dcd_fn)
step = 1
l = mddb_parser.get_trjectory_length(pdb_fn, trj_fn)
chunk_size = 10
num_chunks = int(math.ceil(float(l)/chunk_size))
cur = conn.cursor()
for i in xrange(0, num_chunks):
start = i * chunk_size
stop = min(start + chunk_size, l)
print "trj_id: ", trj_id, " range: ", start, "->", stop \
," total: ", l, " time: ", datetime.datetime.now()
st_io = mddb_parser.parse_trajectory_range_to_buffer(trj_id, pdb_fn, trj_fn, start, stop, step)
cur = conn.cursor()
cur.copy_from(st_io, 'AtomPositions', columns=('trj_id', 't', 'atom_id', 'x', 'y', 'z'))
cur.close()
conn.commit()
return
def load(self, conn, result_dir, d, local_paths):
d['prefix'] = result_dir
out_fns = self.__class__.get_output_fns(d)
trj_id = d['trj_id']
e_id = d['e_id']
sim_fn = out_fns['sim_fn']
trj_fn = out_fns['trj_fn']
nrg_fn = out_fns['nrg_fn']
vel_fn = out_fns.get('vel_fn')
print "simulation file: ", sim_fn
print "trajectory file: ", trj_fn
ap_t_name = 'trj_{0}_ap'.format(trj_id)
pf_t_name = 'trj_{0}_pf'.format(trj_id)
step = 1
l = mddb_parser.get_trjectory_length(sim_fn, trj_fn)
chunk_size = 100000
num_chunks = int(math.ceil(float(l)/chunk_size))
cur = conn.cursor()
for i in xrange(0, num_chunks):
start = i * chunk_size
stop = min(start + chunk_size, l)
print "trj_id: ", trj_id, " range: ", start, "->", stop \
," total: ", l, " time: ", datetime.datetime.now()
crd_st_io = mddb_parser.parse_trajectory_range_to_buffer(trj_id, sim_fn, trj_fn, start, stop, step)
if vel_fn and os.path.isfile(vel_fn):
print "velocity file: ", vel_fn
if os.path.splitext(vel_fn)[1] == '.dcd':
self.__class__.reformat_velocity_dcd(vel_fn)
vel_st_io = mddb_parser.parse_trajectory_range_to_buffer(trj_id, sim_fn, vel_fn, start, stop, step)
if vel_st_io != None:
cur.copy_from(vel_st_io, 'AtomVelocities', columns=('trj_id', 't', 'atom_id', 'x', 'y', 'z'))
if crd_st_io == None:
print "Empty string returned"
return False
st = "select create_NewAtomPositions_table(E'{0}', {1});".format(ap_t_name, trj_id)
cur.execute(st)
cur.copy_from(crd_st_io, ap_t_name, columns=('trj_id', 't', 'atom_id', 'x', 'y', 'z'))
cur.execute('create index {0}Index on {0} (trj_id, t);'.format(ap_t_name))
cur.execute("select compute_features ({0}, E'{1}', E'{2}')".format(e_id, ap_t_name, pf_t_name))
cur.execute('insert into AtomPositions select * from {0}'.format(ap_t_name))
cur.execute('insert into ConformationSpace select * from {0}'.format(pf_t_name))
cur.execute("drop table if exists {0}".format(ap_t_name))
cur.execute("drop table if exists {0}".format(pf_t_name))
with open(nrg_fn, 'r') as ifp:
table_width = len(ifp.readline().split())
ifp.seek(0)
if table_width == 3:
cur.copy_from(ifp, 'Energies', columns=('trj_id', 't', 'total'))
elif table_width == 16:
cur.copy_from(ifp, 'Energies', columns=('trj_id', 't', 'bond', 'angle', 'dihed',
'imprp', 'elect', 'vdw', 'boundary',
'misc', 'kinetic', 'total', 'temp', 'potential',
'total3', 'tempavg'))
cur.close()
conn.commit()
return True