def extract_docking_results(self, file_s, input_file_r, input_file_l):
subprocess.check_output(license.wrap_command(
"moebatch -exec \"db_ExportTriposMOL2 ['dock.mdb', 'lig.mol2', 'mol', []]\"",
'moe'),
shell=True,
executable='/bin/bash')
if os.path.exists('lig.mol2'):
ligname = reader.open(input_file_l).ligname
mol2.update_mol2file('lig.mol2',
'lig-.mol2',
ligname=ligname,
multi=True)
os.remove('lig.mol2')
# get SDF to extract scores
sdffile = 'lig.sdf'
subprocess.check_output(license.wrap_command(
"moebatch -exec \"db_ExportSD ['dock.mdb', '%s', ['mol','S'], []]\""
% sdffile, 'moe'),
shell=True,
executable='/bin/bash')
with open(sdffile, 'r') as sdff:
with open(file_s, 'w') as sf:
for line in sdff:
if line.startswith("> <S>"):
print >> sf, sdff.next().strip()
os.remove(sdffile)
else:
open(file_s, 'w').close()
def extract_docking_results(self, file_s, input_file_r, input_file_l):
"""Extract Glide docking results"""
if os.path.exists('dock_pv.maegz'):
# (1) cmd to extract results
subprocess.check_output(
'glide_sort -r sort.rept dock_pv.maegz -o dock_sorted.mae',
shell=True,
executable='/bin/bash')
# (2) convert to .mol2
subprocess.check_output(
'mol2convert -n 2: -imae dock_sorted.mae -omol2 dock_sorted.mol2',
shell=True,
executable='/bin/bash')
if os.path.exists('dock_sorted.mol2'):
ligname = reader.open(input_file_l).ligname
mol2.update_mol2file('dock_sorted.mol2',
'lig-.mol2',
ligname=ligname,
multi=True)
# extract scores
with open('dock.rept', 'r') as ffin:
with open(file_s, 'w') as ffout:
line = ffin.next()
while not line.startswith('===='):
line = ffin.next()
while True:
line = ffin.next()
if line.strip():
print >> ffout, line[43:51].strip()
else:
break
def __init__(self, args, task='docking'):
# check if config file exist
if os.path.exists(args.config_file):
config = ConfigParser.SafeConfigParser()
config.read(args.config_file)
else:
raise ValueError("Config file %s not found!" % (args.config_file))
# check if ligand file exists
if not os.path.isfile(args.input_file_l):
raise IOError("File %s not found!" % (args.input_file_l))
file_l_abs = os.path.abspath(args.input_file_l)
base = os.path.basename(args.input_file_l)
pref, ext = os.path.splitext(base)
if ext != '.mol2':
raise IOError(
"Ligand file provided with -l option should be in .mol2 format! %s format detected!"
% ext)
nligands = int(
subprocess.check_output('fgrep -c "@<TRIPOS>ATOM" %s' % file_l_abs,
shell=True))
if nligands == 0:
raise IOError("No ligand detected in %s, check your file again!" %
args.input_file_l)
elif nligands > 1:
raise IOError(
"More than one ligand detected in %s. Only one structure per ligand file is allowed!"
% args.input_file_l)
# new ligand file with unique names for every atom
new_file_l = pref + '_dbx' + ext
# create a ligand file with unique atom names
mol2.update_mol2file(file_l_abs,
new_file_l,
unique=True,
ligname='LIG')
self.input_file_l = os.path.abspath(new_file_l)
if task == 'docking':
self.docking = configure.DockingSetup(config)
self.rescoring = configure.RescoringSetup(config)
elif task == 'scoring':
self.scoring = configure.ScoringSetup(config)
else:
raise ValueError("Task should be one of docking or scoring")
self.check_pdbfile(args.input_file_r)
def update_output_mol2files(self, sample=None):
nfiles = len(glob('pose-*.mol2'))
mgltools_path = subprocess.check_output('which prepare_ligand4.py',
shell=True,
executable='/bin/bash')
mgltools_path = '/'.join(mgltools_path.split('/')[:-3])
for idx in range(nfiles):
mol2file = 'pose-%s.mol2' % (idx + 1)
mol2.update_mol2file(mol2file,
mol2file,
ADupdate=sample,
unique=True,
mask=['h', 'H'])
mol2.arrange_hydrogens(mol2file, 'tmp.mol2', path=mgltools_path)
shutil.move('tmp.mol2', mol2file)
def extract_docking_results(self, file_s, input_file_r, input_file_l):
# save scores
if os.path.isfile('lig_out_scored.mol2'):
with open('lig_out_scored.mol2', 'r') as ffin:
with open(file_s, 'w') as ffout:
idx = 0
for line in ffin:
if line.startswith('########## Grid Score:'):
print >> ffout, line.split()[3]
idx += 1
if idx == int(self.options['nposes']):
break
# create multiple mol2 files
ligname = reader.open('lig_out_scored.mol2').ligname
mol2.update_mol2file('lig_out_scored.mol2',
'lig-.mol2',
ligname=ligname,
multi=True,
last=int(self.options['nposes']))
else:
open(file_s, 'w').close()
def extract_docking_results(self, file_s, input_file_r, input_file_l):
for idx, mol2file in enumerate(sorted(glob('gold_soln_*_m1_*.mol2'))):
output_mol2file = 'lig-%s.mol2' % (idx + 1)
mol2.update_mol2file(mol2file, output_mol2file, remove='LP')
