def run_docking_combo_local(job_dict):
r_id = job_dict['r_id']
c_id = job_dict['c_id']
p_id = job_dict['p_id']
cs_id = job_dict['cs_id']
taut = job_dict['taut']
mol_fn = job_dict['mol_fn']
docker = job_dict['docker']
mol_fn_rel = os.path.basename(mol_fn)
sub_dir = "{0}".format(c_id)
if not os.path.exists(in_dir + "/" + sub_dir + "/grid.bmp"):
shutil.copy(in_dir + "/grid.bmp", in_dir + "/" + sub_dir)
if not os.path.exists(in_dir + "/" + sub_dir + "/grid.nrg"):
shutil.copy(in_dir + "/grid.nrg", in_dir + "/" + sub_dir)
if not os.path.exists(in_dir + "/" + sub_dir + "/selected_spheres.sph"):
shutil.copy(in_dir + "/selected_spheres.sph", in_dir + "/" + sub_dir)
head,tail = os.path.splitext(mol_fn)
amber_score_mol_fn = head + ".amber_score" + tail
pdb_fn = "{0}/3D7F_h.pdb".format(in_dir)
recp_fn = "{0}/3D7F.oeb.gz".format(in_dir)
fn_dict = prepare_filenames(job_dict)
dock6_inp = fn_dict['dock6_inp']
dock6_out = fn_dict['dock6_out']
dock6_amber_inp = fn_dict['dock6_amber_inp']
dock6_amber_out = fn_dict['dock6_amber_out']
fred_prefix = fn_dict['fred_prefix']
fred_out = fn_dict['fred_out']
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
if docker == 1:
if not result_exists(conn, "bindingscoresfred", r_id, c_id, p_id, cs_id, taut):
print "==========================================================================="
print "Running fred"
run_fred(recp_fn, mol_fn, fred_prefix, sub_dir)
fred_scores = lddb_parsers.parse_fred(fred_out)
insert_fred_scores(r_id, c_id, p_id, cs_id, taut, fred_scores)
else:
print "Skip fred for {0}".format(mol_fn)
if docker == 2:
if not result_exists(conn, "bindingscoresdock6", r_id, c_id, p_id, cs_id, taut):
print "==========================================================================="
print "Running dock6"
run_dock6(mol_fn_rel, dock6_inp, dock6_out, sub_dir)
dock6_scores = lddb_parsers.parse_dock6(dock6_out)
insert_dock6_scores(r_id, c_id, p_id, cs_id, taut, dock6_scores)
else:
print "Skip dock6 for {0}".format(mol_fn)
if docker == 3:
if not result_exists(conn, "bindingscoresdock6amber", r_id, c_id, p_id, cs_id, taut):
print "==========================================================================="
print "Running dock6 with amber"
run_dock6_with_amber(mol_fn_rel, pdb_fn, dock6_amber_inp, dock6_amber_out, sub_dir)
dock6_amber_scores = lddb_parsers.parse_dock6_amber(dock6_amber_out)
insert_dock6_amber_scores(r_id, c_id, p_id, cs_id, taut, dock6_amber_scores)
else:
print "Skip dock6amber for {0}".format(mol_fn)
return ''
def load(self, conn, prefix, d, local_paths):
#trj_dir = os.path.join(d['dest_dir'], "recp{receptor_id}_model{model_id}/trj{trj_id}".format(**d))
#frame_dir = os.path.join(recpmodel_dir, "frame{t}".format(**d))
frame_dir = d['frame_dir']
grid_fn = 'grid.out'
selected_spheres_fn = 'selected_spheres.sph'
boxpdb_fn = 'step2_box.pdb'
bmp_fn = 'step3_grid_score.bmp'
nrg_fn = 'step3_grid_score.nrg'
if not (os.path.exists(os.path.join(frame_dir, grid_fn)) and \
os.path.exists(os.path.join(frame_dir, selected_spheres_fn)) and \
os.path.exists(os.path.join(frame_dir, bmp_fn)) and \
os.path.exists(os.path.join(frame_dir, nrg_fn)) and \
os.path.exists(os.path.join(frame_dir, boxpdb_fn)) ):
cmd_st = 'cp *grid* *.sph *box* {0}'.format(frame_dir)
subprocess.call(cmd_st, shell = True, cwd = prefix, stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
print 'Copied all to %s' % frame_dir
# Move the docked file to the unique name
original_docked_fn = 'docked_ligand_scored.mol2'
docked_fn = '{0}_level{1}_docked_{2}.mol2'.format(d['docker'], d['docker_level'], d['compoundstate_id'])
cmd_st = 'mv {0} {1}'.format(original_docked_fn, docked_fn)
subprocess.call(cmd_st, shell = True, cwd = prefix, stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
# Copy the docked file to the frame dir
cmd_st = 'cp {0} {1}'.format(docked_fn, frame_dir)
subprocess.call(cmd_st, shell = True, cwd = prefix, stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
d['dest_dir'] = os.path.join(local_paths['resource_prefix'],
d['dbname'])
job_dir = os.path.join(d['dest_dir'], 'job'+str(d['job_id']))
if not os.path.exists(job_dir):
os.makedirs(job_dir)
cmd_st = 'cp * {0}'.format(job_dir)
subprocess.call(cmd_st, shell = True, cwd = prefix, stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
#with open(os.path.join(job_dir, 'job_dict.txt'), 'w') as ofp:
# ofp.write(str(d))
score_fn = os.path.join(job_dir, 'step4_dock6.out')
results = lddb_parsers.parse_dock6(score_fn)
st_out = cStringIO.StringIO()
for r in results:
r = [d['job_id']] + r
r = map(str, r)
st_out.write('\t'.join(r) + '\n')
st_out.seek(0)
cur = conn.cursor()
cur.copy_from(st_out, 'Level1_dock6scores', columns = ('job_id', 'gs', 'gvdw', 'ges', 'inen'))
cur.close()
conn.commit()
return bool(results), job_dir
