def load_trjs_dir(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute("select S.pdb_id from seq_pdb S left join trajectories T on S.pdb_id = T.pdb_id where T.pdb_id is null;")
run_params = cur.fetchall()
cur.close()
conn.close()
wanted_list = map(lambda d: int(d['pdb_id']), run_params)
print wanted_list
trj_dir = '/damsl/projects/{dbname}/trajectories'.format(**self.param_dict)
pdb_id_dirs = os.listdir(trj_dir)
#print pdb_id_dirs
for pdb_id_dir in pdb_id_dirs:
try:
pdb_id_dir = int(pdb_id_dir)
if pdb_id_dir in wanted_list:
d = {'pdb_id': pdb_id_dir, 'trj_prefix': trj_dir}
d.update(self.param_dict)
self.load_trj(d)
else:
print 'pdb_id_dir:', pdb_id_dir, 'is already loaded'
except Exception as e:
print e
pass
def load_one(self):
try:
query = "SELECT jq_entry_id,data FROM loadingqueue ORDER BY jq_entry_id limit 1"
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.execute(query)
row = cur.fetchone()
id = row[0]
data = row[1]
d = eval(data)
self.load_trj(d)
print "Loaded: id"
cur.execute("DELETE FROM loadingqueue WHERE jq_entry_id = %s",(id,))
cur.close()
conn.commit()
conn.close()
return True
except Exception as e:
traceback.print_exc()
print "failed"
return False
def load_receptor_frames(self):
data_dir = '/damsl/projects/molecules/data/Odorant_GPCR/'
frames_fn = os.path.join(data_dir, 'frames.txt')
trajectories_fn = os.path.join(data_dir, 'trajectories.txt')
receptormodels_fn = os.path.join(data_dir, 'receptormodels.txt')
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
with open(receptormodels_fn, 'r') as ifp:
cur.copy_from(ifp, 'ReceptorModels',
columns = ('receptor_id', 'model_id', 'pdb_fn'))
cur.execute('select count(*) from ReceptorModels')
print cur.fetchone()[0], 'receptor models added'
with open(trajectories_fn, 'r') as ifp:
cur.copy_from(ifp, 'Trajectories',
columns = ('receptormodel_id', 'expsolv', 'bilayer', 'trj_dir'))
cur.execute('select count(*) from Trajectories')
print cur.fetchone()[0], 'trajectories added'
with open(frames_fn, 'r') as ifp:
cur.copy_from(ifp, 'Frames',
columns = ('trj_id', 't', 'fred_fn', 'dock6_fn', 'pdb_fn'))
cur.execute('select count(*) from Frames')
print cur.fetchone()[0], 'frames added'
cur.close
conn.commit()
conn.close()
def queue_more_jobs(job_dict):
print "queuing more jobs"
offset = job_dict['offset']
limit = job_dict['limit']
docker = job_dict['docker']
stm = 'select receptor_id, model_id, fred_fn, dock6_fn, compound_id, tautomers, smi_fn, sdf_fn ' +\
'from UnfinishedJobsView J ' +\
'order by job_id ' +\
'offset {0} limit {1}'.format(offset, limit)
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
cur.execute(stm)
rows = cur.fetchall()
job_size = 1
num_entries = len(rows)
groups = list(chunks(rows, job_size))
for rows in groups:
json_st = "[{0}]".format(",".join(rows))
stm = "select queue_gearman_job(E'{0}', E'{1}', E'{2}')".format(
json_st,
gmdhost,
gmdport)
print stm
cur.execute(stm)
cur.close()
conn.commit()
conn.close()
def load_compounds(self):
smi_list_fn = '/damsl/projects/molecules/data/Odorant_GPCR/smi_list.txt'
with open(smi_list_fn, 'r') as ifp:
smi_list = ifp.readlines()
output = StringIO.StringIO()
dict = {}
for f in smi_list:
dir,f = os.path.split(f)
m = re.search('ODL(.+?)_', f)
c_id = int(m.group(1))
t = 'tautomers' in f
if not t:
with open(os.path.join('/damsl/projects',dir, f.rstrip()), 'r') as smi_fp:
smi_st = smi_fp.read().split()[0]
output.write("{0},{1},{2},{3},{4}\n".format(c_id,t, f.rstrip(), smi_st, dir))
output.seek(0)
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.copy_from(output, 'InitialCompounds', sep = ',',
columns = ('compound_id', 'tautomers', 'smi_fn', 'smiles', 'compound_dir'))
cur.execute('select count(*) from InitialCompounds')
print cur.fetchone()[0], 'compounds added'
cur.close
conn.commit()
conn.close()
output.close()
def createjobs(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute("select S.pdb_id from seq_pdb S left join trajectories T on S.pdb_id = T.pdb_id where T.pdb_id is null;")
run_params = cur.fetchall()
cur.execute("truncate table jobqueue")
#cur.execute("truncate table loadingqueue")
for d in run_params:
d['generator'] = 'impsolv'
d['dbname'] = self.param_dict['dbname']
d['dbuser'] = self.param_dict['dbuser']
d['dbhost'] = self.param_dict['dbhost']
d['dbpass'] = self.param_dict['dbpass']
data = 'ARRAY' + str([json.dumps(d)])
cur.execute('select jobqueue_insert({0})'.format(data))
#print d
cur.close()
conn.commit()
conn.close()
def sample_loop(self):
while True:
#try:
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
res = mddb_utils.execute_query(conn,
"select param_value from ControlParams where param_name = 'sampleloop'")
print datetime.datetime.now()
try:
nt = mddb_utils.execute_query(conn, "select resample_blocking(E'{gmdhost}:{gmdport}')".format(**self.param_dict))
except Exception as e:
m = "Error {0}".format(str(e))
print m
try:
mddb_utils.execute_query(conn, "insert into ErrorMessages values (statement_timestamp(),{0},{1})".format("sample_loop", m.encode("utf-8")))
except:
pass
nt = 0
time.sleep(2)
continue
if int(nt) > 0:
time.sleep(0.05)
else:
time.sleep(2)
print res
if res == 'quitting':
mddb_utils.execute_query(conn,
"select controlparams_upsert('sampleloop', 'notrunning')")
mddb_utils.execute_query(conn,
"update ExpJobs set active = False;")
conn.close()
break
cur = conn.cursor()
cur.execute('select S.subspace_id from subspaces S, expjobs E where S.subspace_id = E.subspace_id group by S.subspace_id having bool_or(active)')
num_active_subspaces = cur.rowcount
if num_active_subspaces == 0:
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute('select * from mdq_pop()')
if cur.rowcount > 0:
ss_dict = cur.fetchone()
if any(ss_dict.values()):
ss_dict['protein_seq'] = "".join(ss_dict['expanded_terms'])
mddb_utils.subspace_init(dict(self.param_dict.items() + ss_dict.items()))
cur.close()
conn.commit()
conn.close()
def insert_fred_scores(r_id, c_id, p_id, chargeset, tautomers, scores):
if scores != None and len(scores) != 0:
vals = '({0})'.format(', '.join(map(str, [r_id,c_id, p_id, chargeset, tautomers] + scores)))
stm = "insert into BindingScoresFred values\n{0}".format(vals)
else:
stm = "insert into BindingScoresFred (receptor_id, compound_id, pose_id, chargeset_id, tautomers) " +\
"values ({0},{1},{2},{3},{4})".format(r_id,c_id, p_id, chargeset, tautomers)
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
mddb_utils.execute_query(conn, stm)
def clear_jobqueue(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.execute('truncate table JobQueue')
cur.close()
conn.commit()
conn.close()
def process_work(self):
print "start processing work"
try:
gateway_host = self.resource.gateway_host or 'localhost'
except:
gateway_host = 'localhost'
# session directory is named after the gateway host appended by a random string for uniqueness
session_dir = 's_' + gateway_host + '_' + str(uuid.uuid4())[0:8]
while True:
if self.resource.check_deployments():
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
deployment_size = self.resource.job_concurrency * self.param_dict['avg_seq_jobs']
sql_st = 'select jobqueue_dequeue({0})'.format(deployment_size)
cur.execute(sql_st)
try:
res = cur.fetchone()[0]
job_dicts = map(eval, res)
print datetime.datetime.now()
print res
except:
job_dicts = []
cur.close()
conn.commit()
conn.close()
if job_dicts: # got job, got slot
self.resource.deploy(session_dir, job_dicts, self.param_dict)
if not self.resource.__class__ == resources.LocalResource:
time.sleep(50)
else: # got job, no slot
time.sleep(3)
else: # no slot
time.sleep(3)
#local_paths = resource.LocalResource.get_paths()
# delete the session directory
# shutil.rmtree(session_dir)
return
def insert_dock6_amber_scores(r_id, c_id, p_id, chargeset, tautomers, list_of_score_tups):
if list_of_score_tups != None and len(list_of_score_tups) != 0:
vals = ',\n'.join(
map(lambda x: '({0})'.format(', '.join(map(str, [r_id,c_id, p_id, chargeset, tautomers] + list(x)))), list_of_score_tups)
)
stm = "insert into BindingScoresDock6Amber values\n{0}".format(vals)
else:
stm = "insert into BindingScoresDock6Amber (receptor_id, compound_id, pose_id, chargeset_id, tautomers) " +\
"values ({0},{1},{2},{3},{4})".format(r_id,c_id, p_id, chargeset, tautomers)
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
mddb_utils.execute_query(conn, stm)
def load_configs(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
c_id_all = mddb_utils.execute_query(conn, "select insert_new_config('charmm', 'all')")
self.load_config(c_id_all, '/damsl/mddb/data/amino_configs/config_charmm')
c_id_ua = mddb_utils.execute_query(conn, "select insert_new_config('charmm', 'ua')")
self.load_config(c_id_ua, '/damsl/mddb/data/amino_configs/config_ua_charmm')
#mddb_utils.load_machine_info(conn, ['mddb','mddb2','qp2','qp3','qp4','qp5','qp6'])
conn.commit()
conn.close()
def fetch_results():
st = mddb_utils.run_cmd("ssh hhpc python2.6 nutanong/mddb/scheduler/lddb_sqlite_utils.py --mode getresults")
sql_stms = st.split("\n")
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
cur = conn.cursor()
for stm in sql_stms:
print stm
try:
cur.execute(stm)
except:
pass
conn.commit()
cur.close()
conn.close()
def quit_existing_workers(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.execute("select worker_name from Workers")
for rec in cur:
gw_name = rec[0]
mddb_utils.run_cmd("screen -X -S {0} quit".format(gw_name))
cur.execute("truncate Workers cascade")
cur.execute("select setval((select pg_get_serial_sequence('workers', 'worker_id')), 1, false)")
conn.commit()
cur.close()
conn.close()
def load_trj(self,d):
print d
d2 = copy.deepcopy(self.param_dict)
d2.update(d)
d = d2
print d
pdbid = d['pdb_id']
query = "SELECT SS.subspace_id, SS.seqid FROM seq_pdb SP, seq_subspace SS WHERE SP.pdb_id = %s AND SP.seqid = SS.seqid"
conn = mddb_utils.get_dbconn(d['dbname'],
d['dbuser'],
d['dbhost'],
d['dbpass'])
cur = conn.cursor()
cur.execute(query,(pdbid,))
rows = cur.fetchall()
ss_id = None
seq_id = None
if (len(rows) == 0):
print "Creating New Subspace:"
query = "SELECT seqid from seq_pdb where pdb_id = %s"
cur = conn.cursor()
cur.execute(query,(pdbid,))
seqid = cur.fetchall()[0][0]
cur.close()
self.update_dict(d,pdbid)
self.config_ss()
ss_id = mddb_utils.subspace_init(d)
else:
ss_id = rows[0][0]
seqid = rows[0][1]
self.update_dict(d,pdbid)
mddb_utils.load_trajectories(conn,ss_id,d)
cur.close()
cur = conn.cursor()
query = "INSERT INTO seq_subspace (seqid,subspace_id) VALUES (%s, %s)"
print query
cur.execute(query, (seqid, ss_id))
conn.commit()
print cur.fetchone()[0]
cur.close()
conn.close()
print "Successfuly Loaded Trajectory"
def setup_workers(self, l):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
for d in l:
h = d['hostname']
self.param_dict['res_config_name'] = d.get('res_config_name') or 'default'
self.param_dict['avg_seq_jobs'] = d.get('avg_seq_jobs') or 1
self.prepare_worker(h)
prefix = os.path.join(os.getenv('HOME'),
self.param_dict['user'],
self.param_dict['mwd'])
self.param_dict['remotegen'] = ""
self.param_dict['gen_host'] = h
remote_resource_names = [k for k,v in resources.resource_dict.items() if v != resources.LocalResource]
if h in remote_resource_names:
self.param_dict['worker_host'] = 'localhost'
else:
self.param_dict['worker_host'] = self.param_dict['gen_host']
# centos hosts reqires a different PYTHONPATH than ubuntu hosts
# TODO: add more centos hosts all qp-hm* and qp-hd*
if self.param_dict['worker_host'] in ['mddb', 'mddb2', 'localhost']:
self.param_dict['pythonpaths'] = self.centos_pythonpaths.format(prefix)
else:
self.param_dict['pythonpaths'] = self.ubuntu_pythonpaths.format(prefix)
# insert the worker name into the 'workers' table
i = mddb_utils.execute_query(conn, "select workers_insert('{gen_host}');".format(**self.param_dict))
self.param_dict['worker_id'] = i
self.param_dict['worker_name'] = "gmw_{dbname}_{gen_host}_{worker_id}_{user}".format(**self.param_dict)
self.start_gmw(conn)
conn.commit()
conn.close()
def load_compound_states(self):
self.load_compounds()
prefix = '/damsl/projects/'
taut_cmd = '/damsl/projects/molecules/software/DD/OpenEye/openeye/bin/tautomers'
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute('select compound_dir,smi_fn,compound_id from initialcompounds order by compound_id')
compound_dicts = cur.fetchall()
#cur.execute('truncate table CompoundStates')
for d in compound_dicts:
output = StringIO.StringIO()
cmd = taut_cmd + ' ' + os.path.join(prefix,d['compound_dir'], d['smi_fn'])
taut_fn = '/tmp/tautout{0}.txt'.format(d['compound_id'])
with open(taut_fn, 'w') as ofp:
subprocess.call(cmd, shell=True, stdout=ofp,
cwd=os.environ['HOME']
)
with open(taut_fn, 'r') as ifp:
l = ifp.readlines()
print l
for state_id,compound_state_smi in enumerate(l):
compound_state_smi = compound_state_smi.split()[0]
line = '{0}\t{1}\t{2}\n'.format(d['compound_id'], state_id, compound_state_smi)
print line
output.write(line)
output.seek(0)
cur.copy_from(output, 'CompoundStates', columns = ('compound_id', 'state_id', 'smiles'))
conn.commit()
conn.close()
def queue_jobs(self, jobfile):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
with open(jobfile, 'r') as ifp:
content = ifp.read()
print content
job_obj = ast.literal_eval(content) #json.loads(content, object_hook=mddb_utils.ascii_encode_dict)
print job_obj
job_dicts = controller.Controller.get_job_dicts(**job_obj)
for d in job_dicts:
print 'queue job: ', d
mddb_utils.mdq_push(conn,**d)
#mddb_utils.mdq_push(conn, 0, psp_terms, num_expjobs, num_iterations, num_steps_sim, u_id, policy,
# simulator, config_id)
return
def work(self):
comment = "mode: initdb\nRequired Param: --dbname"
print comment
self.load_stored_procedures(['lddb_utils.sql'])
self.quit_everything()
self.load_stored_procedures(['job_control.sql'])
l = []
l.append({'hostname':'localhost', 'avg_seq_jobs': '1', 'res_config_name': 'def'})
#l.append({'hostname':'stampede', 'avg_seq_jobs': '1', 'res_config_name': 'dev'})
#l.append({'hostname':'lonestar', 'avg_seq_jobs': '1', 'res_config_name': 'mpi'})
self.setup_workers(l)
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute("select * from level1_unfinishedjobsview order by job_id;")
#cur.execute("select * from level1_unfinishedjobsview order by job_id;")
#cur.execute("select 'membrane' as generator,* from unprocessedreceptormodelsview order by receptor_id,model_id;")
run_params = cur.fetchall()
#run_params = run_params[:5]
for d in run_params:
d['dbname'] = self.param_dict['dbname']
data = json.dumps(d)
job_id = d.get('job_id') or 'NULL'
cur.execute("select jobqueue_insert({0},'{1}')".format(job_id, data))
cur.close()
conn.commit()
conn.close()
def __init__(self):
# parse command line arguments
self.param_dict = param_dict_parser.parse(self.param_dict)
print self.param_dict
res_name = self.param_dict.get('gen_host') or 'localhost'
proc_id = os.getpid();
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
# update the worker entry
st = "update Workers set worker_name = '{0}', process_id = {1}, resource_name = '{2}' where worker_id = {3}"
cur.execute(st.format(self.param_dict['worker_name'],
proc_id,
res_name,
self.param_dict['worker_id'],
))
cur.close()
conn.commit()
conn.close()
res_class = resources.resource_dict[res_name]
# init resource object
self.resource = res_class(self.param_dict.get('user'),
self.param_dict.get('res_config_name'),
worker_id = self.param_dict['worker_id'])
print st
print self.param_dict
def start_sampleloop(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
prefix = os.path.join(os.getenv('HOME'),
self.param_dict['user'],
controller.Controller.mwd)
pp = controller.Controller.centos_pythonpaths.format(prefix)
env = "PYTHONPATH={0} GPHOME=/opt/greenplum-db/. PGHOST=localhost4 PGOPTIONS=--client-min-messages=error ".format(pp)
env = env + "PATH={PATH} LD_LIBRARY_PATH={LD_LIBRARY_PATH} ".format(**os.environ)
self.param_dict['env'] = env
sample_loop_cmd = ("""screen -S {dbname}_{user}_sample_loop -d -m """+\
"""env {env}""" +\
"""/opt/greenplum-db/ext/python/bin/python """+ os.path.abspath( __file__ ) +\
""" --mode loop """+\
""" --dbname {dbname} """+\
""" --dbpass {dbpass} """+\
""" 2>&1 | tee /tmp/{dbname}_{user}_sampleloop.log >&1 """).format(**self.param_dict);
mddb_utils.run_cmd(sample_loop_cmd)
mddb_utils.execute_query(conn,
"select controlparams_upsert('sampleloop', 'running')")
conn.commit()
conn.close()
def preprocess(d, local_paths):
d['dest_dir'] = os.path.join(local_paths['resource_prefix'],
d['dbname'])
session_dir = d['session_dir']
#pdb_path = os.path.join('/damsl/projects/molecules/data/PTEN/data/josh/output', seq_id, seq_id+'.B99990001.pdb')
output_prefix = os.path.join(local_paths['resource_prefix'], local_paths['io_dir'], session_dir, d['run_dir'])
conn = mddb_utils.get_dbconn(d['dbname'],
d['dbuser'],
d['dbhost'],
d['dbpass'])
if not os.path.exists(output_prefix):
os.makedirs(output_prefix)
print 'output_prefix: ', output_prefix
if ('sim_input_id' in d):
cur = conn.cursor()
cur.execute('select sim_input_fn from sim_inputs where sim_input_id = {0}').format(d['sim_input_id'])
sim_input_fn = cur.fetchone()['sim_input_fn']
d['charmm_s0in'] = sim_input_fn + '_start,in'
d['charmm_s1in'] = sim_input_fn + '_1,in'
if ('pdb_id' not in d):
# need to do structure prediction. First insert sequence into db
insert_query = "SELECT sequence_insert(%s)"
aaseq = d['aaseq']
fasta = ""
cur1 = conn.cursor()
cur1.execute(insert_query,(fasta,))
rows = cur1.fetchall()
seqid = str(rows[0][0])
d['seqid'] = seqid
cur1.close()
conn.commit()
fasta = ">" + seqid + "\n" + aaseq
update_query = "UPDATE sequences_josh SET fasta=%s where seqid=%s"
cur2 = conn.cursor()
cur2.execute(update_query,(fasta, int(seqid)))
cur2.close()
conn.commit()
# create modeller pdb
# create file names for later use
fastaFileName = output_prefix + seqid + ".fasta"
f = open(fastaFileName,'w+')
f.write(fasta)
f.close()
pirFileName = output_prefix + seqid +'.ali'
# TODO check this
pdbFileName = os.path.join(local_paths['template_prefix'].format("/home/webapp",d['user']),ImpSolvPipeline.template_dir,'1d5r.pdb')
alignFileName = output_prefix + seqid +'-p60484'+ '.ali'
# convert fasta file to pir file
MT.fastaToPir(fastaFileName,pirFileName)
# align pir to pdb file
MT.alignPirToPdb(pirFileName,pdbFileName,seqid,alignFileName)
# insert alignment to DB
MT.dbInsertAlignment(conn, seqid, alignFileName)
# build homology models
MT.doAutoModel(alignFileName,pdbFileName,seqid)
# move output to proper directory
pdbfile = seqid + ".B99990001.pdb"
f = open(pdbfile,'r')
pdb = f.read()
f.close()
insert_query = "SELECT pdb_insert(%s,%s,%s)"
cur1 = conn.cursor()
cur1.execute(insert_query,(seqid,pdb,"modeller"))
rows = cur1.fetchall()
id = rows[0][0]
cur1.close()
conn.commit()
d['pdb_id'] = id
pdb_id = d['pdb_id']
cur = conn.cursor()
cur.execute('select pdb from seq_pdb where pdb_id = {0}'.format(pdb_id));
pdb_content = cur.fetchone()[0]
with open(os.path.join(output_prefix, 'protein0.pdb'), 'w') as ofp:
ofp.write(pdb_content)
cmd0 = 'python /damsl/projects/molecules/software/tools/pdb2pqr/pdb2pqr-1.8/pdb2pqr.py ' +\
'--ffout=charmm --ff=charmm {0} {1}'.format('protein0.pdb', 'protein1.pdb')
# preprocess pdb file
cmd1 = 'python /damsl/projects/molecules/data/PTEN/Full/Charmm/ACE/charmm-gui-model1/add_segid_PTEN.py ' +\
'-f protein1.pdb -o protein2.pdb -p pdb -s ' +\
'/damsl/projects/molecules/data/PTEN/Full/Charmm/ACE/charmm-gui-model1/resids.dat'
cmd2 = "sed 's/ ATOM/ATOM/' protein2.pdb | " +\
"sed 's/CD1 ILE/CD ILE/' | " +\
"sed 's/1CBDISU/ CB CYS/' | " +\
"sed 's/1SGDISU/ SG CYS/' > protein.pdb "
print cmd0
subprocess.call(cmd0, shell=True, cwd = output_prefix)
print cmd1
subprocess.call(cmd1, shell=True, cwd = output_prefix)
print cmd2
subprocess.call(cmd2, shell=True, cwd = output_prefix)
def __init__(self):
self.param_dict = dict(self.param_dict.items() + self.mddb_param_dict.items())
self.add_parser_options(self.param_dict)
self.param_dict = self.parse_param_dict()
if self.param_dict['mode'] == 'initdb':
self.quit_everything()
self.init_database(self.schema_files)
self.load_stored_procedures(self.sp_files)
self.load_configs()
sys.exit(0)
if self.param_dict['mode'] == 'initss':
mddb_utils.subspace_init(self.param_dict)
sys.exit(0)
if self.param_dict['mode'] == 'trjs':
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
mddb_utils.add_trajectories(conn, self.param_dict)
conn.close()
sys.exit(0)
if self.param_dict['mode'] == 'loop':
self.sample_loop()
sys.exit(0)
if self.param_dict['mode'] == 'setup':
self.quit_everything()
#self.clear_jobqueue()
#self.init_database(self.schema_files)
#self.load_stored_procedures(self.sp_files)
#self.load_configs()
l = []
l.append({'hostname':'stampede', 'sequentialism': '1', 'res_config_name': 'gpu'})
self.setup_workers(l)
#self.start_sampleloop()
sys.exit(0)
if self.param_dict['mode'] == 'qjobs':
#trj_id_list = ['137']
#trj_len = 1000
#num_points = 1
#l = map(lambda x: getStartingPoints(x, trj_len, num_points), trj_id_list)
#l = list(itertools.chain(*l))
l = []
timestamps = [(3294, 555, 50), (3264, 5, 50), (3264, 929, 100)]
for ts in timestamps:
l = l + MDDBController.get_prev_timestamps(*ts)
l = map(lambda (trj_id,t): {'trj_id': "{0:03d}".format(trj_id), 't': t}, l)
l = l[99:]
default_params = {'nstep_simulation': 50000000,
'trj_save_freq': 50000,
'source': 'deshaw',
'generator': 'amber',
'template_dir': 'amber_min',
'dbname': self.param_dict['dbname'],
'dbuser': self.param_dict['dbuser'],
'dbhost': self.param_dict['dbhost'],
'dbpass': self.param_dict['dbpass'],
}
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.execute('truncate table jobqueue')
for d in l:
d.update(default_params)
print d
data = 'ARRAY' + str([json.dumps(d)])
cur.execute('select jobqueue_insert({0})'.format(data))
cur.close()
conn.commit()
conn.close()
if self.param_dict['mode'] == 'cmd':
mc = mddb_cmd()
mc.init_conn(self.param_dict)
mc.cmdloop()
sys.exit(0)
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 ''
receptor_id = '3D7F_h'
dbname = options.dbname
dbhost = options.dbhost
dbuser = options.dbuser
dbpass = options.dbpass
remotegen = options.remotegen
gmdhost = options.gmdhost
gmdport = options.gmdport
run_on_gpu = options.run_on_gpu
task_id = options.task_id
worker_name = options.worker_name
worker = CustomGearmanWorker(["{0}:{1}".format(gmdhost,gmdport)])
worker.set_client_id(options.client_id)
worker.register_task(task_id, process_work)
hostname = socket.gethostname()
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
cur = conn.cursor()
sys.stdout.flush()
#cur.execute(st)
cur.close()
conn.commit()
conn.close()
worker.work()