def dock(receptor, resname, rec_outpath, reorder_outpath, init='dock_init'):
init = eval(init)
dock_pm = init.dock_pm
dock_dir = os.path.join(init.data_dir, init.dock_folder)
rec_path = os.path.join(init.data_dir, rec_outpath)
reorder_path = os.path.join(init.data_dir, reorder_outpath)
dock_name = os.path.basename(rec_path).replace('receptor', 'dock')
out_path = os.path.join(dock_dir, receptor, dock_name)
smina_pm = smina_param()
smina_pm.param_load(config.dock_pm[dock_pm])
if not os.path.exists(os.path.dirname(out_path)):
os.makedirs(os.path.dirname(out_path))
kw = {
'receptor': rec_path,
'ligand': reorder_path,
'autobox_ligand': reorder_path,
'out': out_path
}
cmd = smina_pm.make_command(**kw)
cl = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
cl.wait()
return [[
receptor, resname, rec_outpath, reorder_outpath,
os.path.join(init.dock_folder, receptor, dock_name)
]]
def reorder(receptor, resname, rec_path, lig_path):
reorder_dir = FLAGS.reorder_dir
reo_name = os.path.basename(rec_path).replace('receptor','reorder')
receptor = os.path.basename(os.path.dirname(rec_path))
out_path = os.path.join(reorder_dir, receptor, reo_name)
smina_pm = smina_param()
smina_pm.param_load(config.dock_pm['reorder'])
if not os.path.exists(os.path.dirname(out_path)):
os.makedirs(os.path.dirname(out_path))
kw = {
'receptor': rec_path,
'ligand': lig_path,
'autobox_ligand':lig_path,
'out':out_path
}
cmd = smina_pm.make_command(**kw)
cl = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
cl.wait()
return [[receptor, resname, rec_path, out_path]]
def reorder(receptor, resname, rec_path, lig_path, reorder_dir):
"""
reorder atom in ligand
args:
receptor:: str
4 letters pdb id
resname:: str
res id
rec_path:: str
path of splited receptor
lig_path:: str
path of splited ligand
reorder_dir:: str
dir for output file
returns:
receptor:: str
4 letters pdb id
resname:: str
res id
rec_path:: str
path of splited receptor
reorder_path:: str
path of reorder ligand
"""
reo_name = os.path.basename(rec_path).replace('receptor','reorder')
receptor = os.path.basename(os.path.dirname(rec_path))
out_path = os.path.join(reorder_dir, receptor, reo_name)
smina_pm = smina_param()
smina_pm.param_load(config.dock_pm['reorder'])
if not os.path.exists(os.path.dirname(out_path)):
os.makedirs(os.path.dirname(out_path))
kw = {
'receptor': rec_path,
'ligand': lig_path,
'autobox_ligand':lig_path,
'out':out_path
}
cmd = smina_pm.make_command(**kw)
cl = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
cl.wait()
result = [list(map(lambda x:'"'+str(x)+'"',[receptor, resname, rec_path, out_path]))]
print (result)
return result
def dock(receptor, resname, rec_path, reorder_path, dock_pm, dock_dir):
"""
Smina docking
args:
receptor:: str
4 letters pdb id
resname:: str
res id
rec_path:: str
path of splited receptor
reorder_path:: str
path of reorder ligand
dock_pm:: str
docking parameter
dock_dir:: str
dir for output
returns:
receptor:: str
4 letters pdb id
resname:: str
res id
rec_path:: str
path of splited receptor
reorder_path:: str
path of reorder ligand
dock_path:: str
path of docking result
"""
dock_name = os.path.basename(rec_path).replace('receptor','dock')
receptor = os.path.basename(os.path.dirname(rec_path))
out_path = os.path.join(dock_dir, receptor, dock_name)
smina_pm = smina_param()
smina_pm.param_load(config.dock_pm[dock_pm])
if not os.path.exists(os.path.dirname(out_path)):
os.makedirs(os.path.dirname(out_path))
kw = {
'receptor': rec_path,
'ligand': reorder_path,
'autobox_ligand':reorder_path,
'out':out_path
}
cmd = smina_pm.make_command(**kw)
cl = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
cl.wait()
return [list(map(lambda x:'"'+str(x)+'"',[receptor, resname, rec_path, reorder_path, out_path]))]