def call(container, command, cwd='', paths={}, remove=True):
###load container
Client.load(container)
###setup mount point paths
#{"/path/outside":"/path/incontainer"}
volumes = []
if paths:
for key in paths.keys():
volumes.append(key + ':' + paths[key])
###setup command as a list
command_list = shlex.split(command)
###run the container
output = Client.execute(command_list,
bind=volumes,
options=['--pwd', cwd, '--cleanenv'],
stream=True)
try:
###stream the output
for line in output:
yield line.strip()
#catch singularity errors from non-zero exit
#TODO figure out how to read them
except subprocess.CalledProcessError:
pass
def make_separate_directory(file_all, protein, source):
#shutil.rmtree('trajectories')
isdir = os.path.isdir('trajectories')
if isdir == False:
print('Trajectories do not exist')
os.mkdir('trajectories')
else:
print('exist')
for count, file in enumerate(file_all, start=0):
ismod = os.path.isdir(f'./trajectories/model_{count}')
if ismod == False:
os.mkdir(f'./trajectories/model_{count}')
with open(f'./trajectories/model_{count}/position_ligand_{count}.pdbqt', 'w') as file_traj:
file_traj.write(file)
shutil.copy(protein, f'./trajectories/model_{count}/')
# nakopiruje navic potrebna data
shutil.copy(f'{source}/_Xqmin_tmp.in', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/_11_run_tleap.sh', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/_21_run-mm_meta.sh', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/{protein}', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/ligand.prepi', f'./trajectories/model_{count}/')
try:
subprocess.run(f'rm ./trajectories/model_{count}/emin2*', shell = True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.inpcrd', shell = True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.prmtop', shell = True)
except:
pass
# convert traj_position_ligand_{count}.pdbqt to pdb -> singularity
Client.load('/home/petrahrozkova/Stažené/caverdock_1.1.sif')
Client.execute(['/opt/mgltools-1.5.6/bin/pythonsh',
'/opt/mgltools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py',
'-f',os.getcwd()+'/trajectories/model_'+str(count)+'/position_ligand_*.pdbqt',
'-o', os.getcwd()+'/trajectories/model_'+str(count)+'/ligand.pdb'])
subprocess.call(f'sed -i \'s/<0> d/TIP d/g\' ./trajectories/model_{count}/ligand.pdb', shell = True) #ligand_for_complex.pdb
subprocess.call(f'tail -n +2 \"./trajectories/model_{count}/ligand.pdb\" > '
f'\"./trajectories/model_{count}/ligand_for_complex.pdb\"', shell = True)
# spojit 'hloupe" ligand, protein do complex.pdb
subprocess.call( #remove last line in file with END. IMPORTANT!
f'head -n -1 ./trajectories/model_{count}/{protein} > ./trajectories/model_{count}/complex.pdb | '
f'echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(f'cat ./trajectories/model_{count}/ligand_for_complex.pdb'
f' >> ./trajectories/model_{count}/complex.pdb ',
#f'| echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(f'echo END >> ./trajectories/model_{count}/complex.pdb',
shell=True)
def run(self, cmd, bind_dir):
self._make_dir()
self._pull_image()
client.load(os.path.join(self.img_dir, self.img_name))
output = client.execute(cmd,
bind=bind_dir + ":/data",
options=['--pwd', '/data', '--cleanenv'],
stream=True)
return output
def run_case(image_dir, image_name, testcase_dir):
client.load(os.path.join(image_dir, image_name))
output = client.execute(
['mpirun', '-np', '6', '/SU2/bin/SU2_CFD', 'Jones.cfg'],
bind=testcase_dir + ":/data:",
options=['--pwd', '/data'],
stream=True)
for val in output:
print(val.strip('\n'))
def run(self, cmd, cores, cfg, log):
self._pull_image()
client.load(os.path.join(self.image_dir, self.image_name))
totalcmd = ['mpirun', '-np', str(cores), '/SU2/bin/' + cmd, cfg.fname]
output = client.execute(
totalcmd,
bind=','.join([self.case_dir + ":/data",
self.mesh_dir + ":/mesh"]),
options=['--pwd', '/data', '--cleanenv'],
stream=True)
with open(log.fname, 'w', buffering=10) as lfile:
for line in output:
lfile.write(line)
def remove_ligand_from_emin(protein, verbose, configfile):
# ted defaultne vypocitany emin5.pdb
with open(protein) as oldfile, open('protein.pdb', 'w+') as newfile:
for line in oldfile:
if not configfile["LIGAND"]["name"] in line:
newfile.write(line)
# convert pdb to pdbqt
prepare_receptor = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load(configfile["SINGULARITY"]["singularity"])
prepare_receptor = Client.execute([
configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"], '-r',
'protein.pdb'
])
if verbose:
print(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
if not os.path.isfile('protein.pdbqt'):
logging.error(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n Message: \n {prepare_receptor}'
)
if verbose:
print(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n {prepare_receptor}'
)
sys.exit(1)
else:
subprocess.call(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb',
shell=True)
logging.info(
f'Run prepare_receptor. Message: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb '
)
if verbose:
print(
f'{configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
print(f'Message{prepare_receptor}')
if not os.path.isfile('protein.pdbqt'):
logging.error(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb \n'
)
if verbose:
print(
f'Cannot run prepare_receptor. Try: \n {configfile["PREPARE_RECEPTOR"]["path_prepare_receptor"]} -r protein.pdb'
)
sys.exit(1)
check_exist_file('protein.pdbqt')
def call(container, command, cwd='', paths={}, remove=True):
###load container
container = 'docker://' + container
Client.load(container)
###setup mount point paths
#{"/path/outside":"/path/incontainer"}
volumes = []
if paths:
for key in paths.keys():
volumes.append(key + ':' + paths[key])
###setup command as a list
command_list = command.split()
###run the container
output = Client.execute(command_list,
bind=volumes,
writable=True,
options=['--pwd', cwd])
#once container is finished return output as a string
return output
def run_cd_energy_profile(tunnel, traj, configfile, verbose):
file = ''
try:
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load(str(configfile['SINGULARITY']['singularity']))
if verbose:
print(
f'{configfile["CD-ENERGYPROFILE"]["path_cd-energyprofile"]} -d {os.getcwd()}/{str(tunnel)} -t {str(traj)} -s {str(configfile["CPU"]["cpu"])}'
)
if int(configfile["SINGULARITY"]["value"]) == 1:
file = Client.execute([
'cd-energyprofile', '-d',
os.getcwd() + '/' + str(tunnel), '-t',
str(traj), '-s',
str(configfile['CPU']['cpu'])
])
with open(f'{os.getcwd()}/energy.dat', 'w') as file_energy_dat:
file_energy_dat.write(str(file))
else:
subprocess.call(
f'{configfile["CD-ENERGYPROFILE"]["path_cd-energyprofile"]} -d {os.getcwd()}/{str(tunnel)} -t {str(traj)} -s {str(configfile["CPU"]["cpu"])} > energy.dat',
shell=True)
if verbose:
print(f'Message from cd-energyprofile: \n {file}')
logging.info(f'Message from cd-energyprofieL: \n {file}')
except:
if verbose:
print('cd-energyprofile returncode is not 0. Check logfile.')
logging.error(f'cd-energyprofile returncode is not 0.')
sys.exit(1)
if not os.path.exists('energy.dat'):
logging.error(f'Cannot make energy.dat')
if verbose:
print('Energy.dat not exists')
sys.exit(1)
def build_to_singularity(definition_entry, container_location):
"""Builds a Singularity container from a Dockerfile or Singularity file
within the definition db.
Parameters:
definition_entry (str): Entry of definition db entry to build singularity container from.
container_location (str): Path to location to build the container.
Returns:
container_location: Returns the location of the Singularity container or None if it
fails to save.
"""
definition_id = definition_entry["definition_id"]
pull_s3_dir(definition_id)
Client.load(PROJECT_ROOT + definition_id)
Client.build(image=os.path.join(PROJECT_ROOT, container_location),
sudo=False)
shutil.rmtree(PROJECT_ROOT + definition_id)
#TODO Find a better way to error check
if os.path.exists(PROJECT_ROOT + container_location):
logging.info(f"Successfully built {container_location}")
return container_location
else:
return None
def run_caverdock(ligand, tunnel, configfile, verbose):
# IN: protein, ligand, tunel
# OUT: pdbqt file with lb and ub
prepare_conf = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
singularity = Client.load(str(
configfile["SINGULARITY"]["singularity"]))
logging.info(
f'Singularity for caverdock: {configfile["SINGULARITY"]["singularity"]} \n'
)
logging.info(f'Message from singularity: \n {singularity}')
if verbose:
print(
f'Singularity for caverdock: {configfile["SINGULARITY"]["singularity"]} \n'
)
print(f'Message from singularity: \n {singularity} \n')
prepare_conf = Client.execute([
configfile["CD-PREPARECONF"]["path_cd-prepareconf"], '-r',
'protein.pdbqt', '-l',
str(ligand), '-t',
str(tunnel)
])
with open('caverdock.conf', 'w+') as file_conf:
file_conf.write(prepare_conf)
if not os.path.isfile('caverdock.conf'):
logging.error(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
logging.error(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'ERROR: {configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
print(f'ERROR: Message from cd-prepareconf: \n {prepare_conf}')
sys.exit(1)
else:
subprocess.call(
f'{configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf',
shell=True)
logging.info(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#logging.info(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'{configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#print(f'Message from cd-prepareconf: \n {prepare_conf}')
if not os.path.isfile('caverdock.conf'):
logging.error(
f'cd-prepareconf -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#logging.error(f'Message from cd-prepareconf: \n {prepare_conf}')
if verbose:
print(
f'ERROR: {configfile["CD-PREPARECONF"]["path_cd-prepareconf"]} -r protein.pdbqt -l {ligand} -t {tunnel} > caverdock.conf'
)
#print(f'ERROR: Message from cd-prepareconf: \n {prepare_conf}')
sys.exit(1)
mpirun = ''
if int(configfile["SINGULARITY"]["value"]) == 1:
mpirun = Client.execute([
'mpirun', '-np', configfile["CPU"]["cpu"], 'caverdock', '--config',
'caverdock.conf', '--out',
str(configfile["RESULT_CD"]["name"])
])
else:
subprocess.call(
f'/usr/bin/mpirun.mpich -np {str(configfile["CPU"]["cpu"])} {configfile["CAVERDOCK"]["path_caverdock"]} --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}',
shell=True)
logging.info(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
logging.info(f'Message from mpirun: \n {mpirun}')
if verbose:
print(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
print(f'Message from mpirun: \n {mpirun}')
if not (os.path.isfile(f'{configfile["RESULT_CD"]["name"]}-lb.pdbqt')
or os.path.isfile(f'{configfile["RESULT_CD"]["name"]}-ub.pdbqt')):
print(f'{configfile["RESULT_CD"]["name"]}-lb.pdbqt')
logging.error(
f'mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
logging.error(f'Message from mpirun: \n {mpirun}')
if verbose:
print(
f'ERROR: mpirun -np {str(configfile["CPU"]["cpu"])} caverdock --config caverdock.conf --out {str(configfile["RESULT_CD"]["name"])}'
)
print(f'ERROR: Message from mpirun: \n {mpirun}')
sys.exit(1)
def make_separate_directory(file_all, protein, source, configfile):
try:
shutil.rmtree('trajectories')
isdir = False
except:
isdir = os.path.isdir('trajectories')
if isdir == False:
print('Trajectories do not exist')
os.mkdir('trajectories')
else:
print('exist')
for count, file in enumerate(file_all, start=0):
ismod = os.path.isdir(f'./trajectories/model_{count}')
if ismod == False:
os.mkdir(f'./trajectories/model_{count}')
with open(
f'./trajectories/model_{count}/position_ligand_{count}.pdbqt',
'w') as file_traj:
file_traj.write(file)
shutil.copy(protein, f'./trajectories/model_{count}/')
# nakopiruje navic potrebna data
#shutil.copy(f'{source}/_11_run_tleap', f'./trajectories/model_{count}/')
#shutil.copy(f'{source}/_21_run_prepare_sander', f'./trajectories/model_{count}/')
shutil.copy(f'{source}/{protein}', f'./trajectories/model_{count}/')
try:
subprocess.run(f'rm ./trajectories/model_{count}/emin*',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.inpcrd',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/complex.prmtop',
shell=True)
except:
pass
try:
subprocess.run(f'rm ./trajectories/model_{count}/ligand.prepi',
shell=True)
except:
pass
# convert traj_position_ligand_{count}.pdbqt to pdb -> singularity
if int(configfile["SINGULARITY"]["value"]) == 1:
Client.load('/home/petrahrozkova/Stažené/caverdock_1.1.sif')
Client.execute([
'/opt/mgltools-1.5.6/bin/pythonsh',
'/opt/mgltools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py',
'-f',
os.getcwd() + '/trajectories/model_' + str(count) +
'/position_ligand_*.pdbqt', '-o',
os.getcwd() + '/trajectories/model_' + str(count) +
'/ligand_H.pdb'
])
else:
subprocess.call(
f'{configfile["PDBQT_TO_PDB"]["path_pdbqt_to_pdb"]} -f {os.getcwd()}/trajectories/model_{str(count)}/position_ligand_{str(count)}.pdbqt '
f'-o {os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb')
subprocess.call(
f'sed -i \'s/<0> d/{configfile["LIGAND"]["name"]} d/g\' ./trajectories/model_{count}/ligand_H.pdb',
shell=True) #ligand_for_complex.pdb
#subprocess.call(f'pdb4amber -i ./trajectories/model_{count}/ligand_H.pdb -o ./trajectories/model_{count}/ligand.pdb --nohyd', shell = True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand_H.pdb')
#subprocess.call(f'antechamber -i {ligand} -fi pdbqt -o ligand.pdb -if pdb', shell = True)
subprocess.call(
f'antechamber -i ./trajectories/model_{count}/ligand_H.pdb -fi pdb -o ./trajectories/model_{count}/ligand.prepi -fo prepi',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/ligand.prepi')
subprocess.call(
f'cat \"./trajectories/model_{count}/ligand_H.pdb\" > '
f'\"./trajectories/model_{count}/ligand_for_complex.pdb\"',
shell=True)
# split (ugly) ligand and protein into complex.pdb
subprocess.call(
f'pdb4amber -i ./trajectories/model_{count}/{protein} -o ./trajectories/model_{count}/protein_w_H.pdb --nohyd',
shell=True)
subprocess.call( #remove last line in file with END. IMPORTANT!
f'head -n -1 ./trajectories/model_{count}/protein_w_H.pdb > ./trajectories/model_{count}/complex.pdb | '
f'echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(
f'cat ./trajectories/model_{count}/ligand_for_complex.pdb'
f' >> ./trajectories/model_{count}/complex.pdb ',
#f'| echo TER >> ./trajectories/model_{count}/complex.pdb',
shell=True)
subprocess.call(
f'echo END >> ./trajectories/model_{count}/complex.pdb',
shell=True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/complex.pdb')
print(f'{os.getcwd()}')
#subprocess.call(f'pdb4amber -i ./trajectories/model_{count}/complex_H.pdb -o ./trajectories/model_{count}/complex.pdb --nohyd', shell = True)
check_exist_file(
f'{os.getcwd()}/trajectories/model_{str(count)}/complex.pdb')
