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docking.py
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import os
import sys
import subprocess
from multiprocessing import Manager
from multiprocessing import Process
from multiprocessing import Queue
from openbabel import pybel
class DockingVina(object):
"""
python module for Vina
"""
def __init__(self, docking_params):
"""
Construction Docking object
put parameters with dictionary
docking_params['vina_program']
docking_params['receptor_file']
docking_params['box_parameter']
(self.box_center, self.box_size) = box_parameter
docking_params['temp_dir']
docking_params['exhaustiveness']
docking_params['num_sub_proc']
docking_params['num_cpu_dock']
docking_params['num_modes']
docking_params['timeout_gen3d']
docking_params['timeout_dock']
"""
super(DockingVina, self).__init__()
self.vina_program = docking_params['vina_program']
self.receptor_file = docking_params['receptor_file']
box_parameter = docking_params['box_parameter']
(self.box_center, self.box_size) = box_parameter
self.temp_dir = docking_params['temp_dir']
self.exhaustiveness = docking_params['exhaustiveness']
self.num_sub_proc = docking_params['num_sub_proc']
self.num_cpu_dock = docking_params['num_cpu_dock']
self.num_modes = docking_params['num_modes']
self.timeout_gen3d = docking_params['timeout_gen3d']
self.timeout_dock = docking_params['timeout_dock']
if not os.path.exists(self.temp_dir):
os.makedirs(self.temp_dir)
def gen_3d(self, smi, ligand_mol_file):
"""
generate initial 3d conformation from SMILES
input :
SMILES string
ligand_mol_file (output file)
"""
run_line = 'obabel -:%s --gen3D -O %s' % (smi, ligand_mol_file)
result = subprocess.check_output(run_line.split(),
stderr=subprocess.STDOUT,
timeout=self.timeout_gen3d, universal_newlines=True)
def docking(self, receptor_file, ligand_mol_file, ligand_pdbqt_file, docking_pdbqt_file):
"""
run_docking program using subprocess
input :
receptor_file
ligand_mol_file
ligand_pdbqt_file
docking_pdbqt_file
output :
affinity list for a input molecule
"""
ms = list(pybel.readfile("mol", ligand_mol_file))
m = ms[0]
m.write("pdbqt", ligand_pdbqt_file, overwrite=True)
run_line = '%s --receptor %s --ligand %s --out %s' % (self.vina_program,
receptor_file, ligand_pdbqt_file, docking_pdbqt_file)
run_line += ' --center_x %s --center_y %s --center_z %s' %(self.box_center)
run_line += ' --size_x %s --size_y %s --size_z %s' %(self.box_size)
run_line += ' --cpu %d' % (self.num_cpu_dock)
run_line += ' --num_modes %d' % (self.num_modes)
run_line += ' --exhaustiveness %d ' % (self.exhaustiveness)
result = subprocess.check_output(run_line.split(),
stderr=subprocess.STDOUT,
timeout=self.timeout_dock, universal_newlines=True)
result_lines = result.split('\n')
check_result = False
affinity_list = list()
for result_line in result_lines:
if result_line.startswith('-----+'):
check_result = True
continue
if not check_result:
continue
if result_line.startswith('Writing output'):
break
if result_line.startswith('Refine time'):
break
lis = result_line.strip().split()
if not lis[0].isdigit():
break
# mode = int(lis[0])
affinity = float(lis[1])
affinity_list += [affinity]
return affinity_list
def creator(self, q, data, num_sub_proc):
"""
put data to queue
input: queue
data = [(idx1,smi1), (idx2,smi2), ...]
num_sub_proc (for end signal)
"""
for d in data:
idx = d[0]
dd = d[1]
q.put((idx, dd))
for i in range(0, num_sub_proc):
q.put('DONE')
def docking_subprocess(self, q, return_dict, sub_id=0):
"""
generate subprocess for docking
input
q (queue)
return_dict
sub_id: subprocess index for temp file
"""
while True:
qqq = q.get()
if qqq == 'DONE':
break
(idx, smi) = qqq
# print(smi)
receptor_file = self.receptor_file
ligand_mol_file = '%s/ligand_%s.mol' % (self.temp_dir, sub_id)
ligand_pdbqt_file = '%s/ligand_%s.pdbqt' % (self.temp_dir, sub_id)
docking_pdbqt_file = '%s/dock_%s.pdbqt' % (self.temp_dir, sub_id)
try:
self.gen_3d(smi, ligand_mol_file)
except Exception as e:
# print(e)
# print("gen_3d unexpected error:", sys.exc_info())
# print("smiles: ", smi)
return_dict[idx] = 99.0
continue
try:
affinity_list = self.docking(receptor_file, ligand_mol_file,
ligand_pdbqt_file, docking_pdbqt_file)
except Exception as e:
#print(e)
# print("docking unexpected error:", sys.exc_info())
# print("smiles: ", smi)
return_dict[idx] = 99.0
continue
if len(affinity_list)==0:
affinity_list.append(99.0)
affinity = affinity_list[0]
return_dict[idx] = affinity
def __call__(self, smiles_list):
"""
input SMILES list
output affinity list corresponding to the SMILES list
if docking is fail, docking score is 99.0
"""
data = list(enumerate(smiles_list))
q1 = Queue()
manager = Manager()
return_dict = manager.dict()
proc_master = Process(target=self.creator,
args=(q1, data, self.num_sub_proc))
proc_master.start()
# create slave process
procs = []
for sub_id in range(0, self.num_sub_proc):
proc = Process(target=self.docking_subprocess,
args=(q1, return_dict, sub_id))
procs.append(proc)
proc.start()
q1.close()
q1.join_thread()
proc_master.join()
for proc in procs:
proc.join()
keys = sorted(return_dict.keys())
affinity_list = list()
for key in keys:
affinity = return_dict[key]
affinity_list += [affinity]
return affinity_list