def run(self, input_params):
trj_id = input_params['trj_id']
new_dict = self.run_min(input_params)
print input_params
in_fn = new_dict['simulation_in_fn']
bin = new_dict['charmm_bin']
log_fn = in_fn + '.log'
nrg_fn = log_fn + '.nrg'
mddb_utils.run_cmd_with_file(bin, in_fn, log_fn)
st_io = self.parse_energies(log_fn, trj_id)
with open(nrg_fn, 'w') as ofp:
ofp.write(st_io.getvalue())
def run_min(self, script_params):
done_min = False
count = 1
start_from_anywhere = False
start_from_anywhere = False
phi_psi_array = script_params['phi_psi_array']
if len(phi_psi_array) == 0:
phi_psi_array = map(lambda x: (-math.pi + random.random()*math.pi*2),
[None] * (len(script_params['protein_seq'])-1)*2)
script_params['phi_psi_array'] = phi_psi_array
start_from_anywhere = True
"""Run Minimization using Charmm by default"""
new_job_dict = None
while True:
new_job_dict = genpep.generate_scripts(script_params)
pdb_fn = new_job_dict['pdb_file_name']
if os.path.isfile(pdb_fn):
mddb_utils.run_cmd_with_retries("rm {0}".format(pdb_fn), 1000)
minimization_in_fn = new_job_dict['minimization_in_fn']
while True:
try:
charmm_bin = script_params['charmm_bin']
st =mddb_utils.run_cmd_with_file(charmm_bin,
minimization_in_fn, minimization_in_fn+".log")
break
except Exception, e:
print str(e)
time.sleep(0.2)
if not os.path.isfile(pdb_fn):
time.sleep(0.5)
else:
done_min = os.path.getsize(pdb_fn) > 0
if done_min:
break
neg_or_pos = [-1,1]
print "Trial {0}: {1} {2}".format(count, script_params['phi_psi_array'], done_min)
count = count + 1
if count < 50 and not start_from_anywhere:
delta_phipsi = map(lambda x: neg_or_pos[random.randint(0,1)] * (random.uniform(0,10)*math.pi/180),
[None] * (len(script_params['protein_seq'])-1)*2)
script_params['phi_psi_array'] = map(lambda a,b: a-b, script_params['phi_psi_array'], delta_phipsi)
else:
sign = neg_or_pos[random.randint(0,1)]
script_params['phi_psi_array'] = map(lambda x: sign* (-math.pi + random.randint(4,15)*math.pi/24),
[None] * (len(script_params['protein_seq'])-1)*2)
