def run_ligprep(self, smiles: list):
"""
Call ligprep to prepare molecules.
:param smiles: List of SMILES strings
"""
ligprep_commands = []
# Write out smiles to sdf files and prepare ligprep commands
for smi, name in zip(smiles, self.file_names):
smi_in = os.path.join(self.directory, f'{name}.smi')
sdf_out = os.path.join(self.directory, f'{name}_ligprep.sdf')
with open(smi_in, 'w') as f:
f.write(smi)
command = " ".join(
(self.ligprep_env, f"-ismi {smi_in}", f"-osd {sdf_out}",
"-ph 7.0", "-pht 1.0", "-bff 16", "-s 8", "-epik", "-WAIT",
"-NOJOBID"))
ligprep_commands.append(command)
# Initialize subprocess
logger.debug('LigPrep called')
p = timedSubprocess(timeout=self.timeout).run
# Run commands either using Dask or sequentially
if self.cluster is not None:
futures = self.client.map(p, ligprep_commands)
_ = self.client.gather(futures)
else:
_ = [p(command) for command in ligprep_commands]
logger.debug('LigPrep finished')
return self
def dock_ligands(self, ligand_paths):
smina_commands = []
log_paths = []
for l in ligand_paths:
out_file = os.path.join(
self.directory,
os.path.basename(l).replace("_gypsum.sdf", "_docked.sdf"))
out_log = os.path.join(
self.directory,
os.path.basename(l).replace("_gypsum.sdf", "_log.txt"))
log_paths.append(out_log)
cmd = f"smina -r {self.receptor} -l {l} --autobox_ligand {self.ref} -o {out_file} " \
f"--cpu {self.cpus} --exhaustiveness 8 --energy_range 3 --min_rmsd_filter 1 --quiet " \
f"--log {out_log}"
smina_commands.append(cmd)
# Initialize subprocess
logger.debug('Smina called')
p = timedSubprocess(timeout=self.timeout).run
if self.cluster is not None:
futures = self.client.map(p, smina_commands)
_ = self.client.gather(futures)
else:
_ = [p(command) for command in smina_commands]
logger.debug('Smina finished')
return log_paths
def run_glide(self):
"""
Write GLIDE new input files and submit each to Glide
"""
glide_commands = []
for name in self.file_names:
for variant in self.variants[name]:
# Set some file paths
glide_in = self.glide_options.copy()
# Change glide_in file
glide_in = self.modify_glide_in(
glide_in, 'LIGANDFILE',
os.path.join(self.directory,
f'{name}-{variant}_ligprep.sdf'))
glide_in = self.modify_glide_in(glide_in, 'OUTPUTDIR',
os.path.join(self.directory))
# Write new input file (.in)
with open(os.path.join(self.directory, f'{name}-{variant}.in'),
'wt') as f:
[f.write(line) for line in glide_in]
# Prepare command line command
command = self.glide_env + ' -WAIT -NOJOBID -NOLOCAL ' + \
os.path.join(self.directory, f'{name}-{variant}.in')
glide_commands.append(command)
# Initialize subprocess
logger.debug('Glide called')
p = timedSubprocess(timeout=self.timeout).run
if self.cluster is not None:
futures = self.client.map(p, glide_commands)
_ = self.client.gather(futures)
else:
_ = [p(command) for command in glide_commands]
logger.debug('Glide finished')
return self