def launch(self) -> int:
"""Launches the execution of the GROMACS solvate module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path,
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
if self.container_path:
shutil.copytree(
top_dir,
str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name)))
top_file = str(
Path(self.container_volume_path).joinpath(
Path(top_dir).name,
Path(top_file).name))
cmd = [
self.gmx_path, 'solvate', '-cp',
container_io_dict["in"]["input_solute_gro_path"], '-cs',
self.input_solvent_gro_path, '-o',
container_io_dict["out"]["output_gro_path"], '-p', top_file
]
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
if self.container_path:
top_file = str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name,
Path(top_file).name))
# zip topology
fu.log(
'Compressing topology to: %s' %
container_io_dict["out"]["output_top_zip_path"], out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"],
top_file=top_file,
out_log=out_log)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS pdb2gmx module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
output_top_path = fu.create_name(prefix=self.prefix,
step=self.step,
name=self.output_top_path)
output_itp_path = fu.create_name(prefix=self.prefix,
step=self.step,
name=self.output_itp_path)
cmd = [
self.gmx_path, "pdb2gmx", "-f",
container_io_dict["in"]["input_pdb_path"], "-o",
container_io_dict["out"]["output_gro_path"], "-p", output_top_path,
"-water", self.water_type, "-ff", self.force_field, "-i",
output_itp_path
]
if self.his:
cmd.append("-his")
cmd = ['echo', self.his, '|'] + cmd
if self.ignh:
cmd.append("-ignh")
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
if self.container_path:
output_top_path = os.path.join(container_io_dict.get("unique_dir"),
output_top_path)
# zip topology
fu.log(
'Compressing topology to: %s' %
container_io_dict["out"]["output_top_zip_path"], out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"],
top_file=output_top_path,
out_log=out_log)
tmp_files.append(self.output_top_path)
tmp_files.append(self.output_itp_path)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS make_ndx module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
'echo', '-e', '\'' + self.selection + '\\nq' + '\'', '|',
self.gmx_path, 'make_ndx', '-f',
container_io_dict["in"]["input_structure_path"], '-o',
container_io_dict["out"]["output_ndx_path"]
]
if container_io_dict["in"].get("input_ndx_path")\
and Path(container_io_dict["in"].get("input_ndx_path")).exists():
cmd.append('-n')
cmd.append(container_io_dict["in"].get("input_ndx_path"))
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self):
"""Launches the execution of the template_container module."""
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check the properties
fu.check_properties(self, self.properties)
# Restart
if self.restart:
# 4. Include here all output file paths
output_file_list = [self.io_dict['out']['output_file_path']]
if fu.check_complete_files(output_file_list):
fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
return 0
# 5. Copy inputs to container
container_io_dict = fu.copy_to_container(self.container_path, self.container_volume_path, self.io_dict)
# 6. Prepare the command line parameters as instructions list
instructions = ['-j']
if self.boolean_property:
instructions.append('-v')
fu.log('Appending optional boolean property', out_log, self.global_log)
# 7. Build the actual command line as a list of items (elements order will be maintained)
cmd = [self.executable_binary_property,
' '.join(instructions),
container_io_dict['out']['output_file_path'],
container_io_dict['in']['input_file_path1']]
fu.log('Creating command line with instructions and required arguments', out_log, self.global_log)
# 8. Repeat for optional input files if provided
if container_io_dict['in']['input_file_path2']:
# Append optional input_file_path2 to cmd
cmd.append(container_io_dict['in']['input_file_path2'])
fu.log('Appending optional argument to command line', out_log, self.global_log)
# 9. Uncomment to check the command line
# print(' '.join(cmd))
# 10. Create cmd with specdific syntax according to the required container
cmd = fu.create_cmd_line(cmd, container_path=self.container_path,
host_volume=container_io_dict.get('unique_dir'),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_image=self.container_image,
container_shell_path=self.container_shell_path,
out_log=out_log, global_log=self.global_log)
# Launch execution
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()
# Copy output(s) to output(s) path(s) in case of container execution
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
# Remove temporary file(s)
if self.remove_tmp and container_io_dict.get('unique_dir'):
fu.rm(container_io_dict.get('unique_dir'))
fu.log('Removed: %s' % str(container_io_dict.get('unique_dir')), out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS select module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'select', '-s',
container_io_dict["in"]["input_structure_path"], '-on',
container_io_dict["out"]["output_ndx_path"]
]
if container_io_dict["in"].get("input_ndx_path") and pl.Path(
container_io_dict["in"].get("input_ndx_path")).exists():
cmd.append('-n')
cmd.append(container_io_dict["in"].get("input_ndx_path"))
cmd.append('-select')
cmd.append("\'" + self.selection + "\'")
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
if self.container_path:
if self.container_path.endswith('singularity'):
fu.log('Using Singularity image %s' % self.container_image,
out_log, self.global_log)
cmd = [
self.container_path, 'exec', '--bind',
container_io_dict.get("unique_dir") + ':' +
self.container_volume_path, self.container_image,
" ".join(cmd)
]
elif self.container_path.endswith('docker'):
fu.log('Using Docker image %s' % self.container_image, out_log,
self.global_log)
docker_cmd = [
self.container_path,
'run',
]
if self.container_working_dir:
docker_cmd.append('-w')
docker_cmd.append(self.container_working_dir)
if self.container_volume_path:
docker_cmd.append('-v')
docker_cmd.append(
container_io_dict.get("unique_dir") + ':' +
self.container_volume_path)
if self.container_user_id:
docker_cmd.append('--user')
docker_cmd.append(self.container_user_id)
docker_cmd.append(self.container_image)
docker_cmd.append(" ".join(cmd))
cmd = docker_cmd
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS grompp module.
Examples:
This is a use example of how to use the Grommpp module from Python
>>> from biobb_md.gromacs.grompp import Grompp
>>> prop = { 'mdp':{ 'type': 'minimization', 'emtol':'500', 'nsteps':'5000'}}
>>> Grompp(input_gro_path='/path/to/myStructure.gro', input_top_zip_path='/path/to/myTopology.zip', output_tpr_path='/path/to/NewCompiledBin.tpr', properties=prop).launch()
"""
tmp_files = []
mdout = 'mdout.mdp'
tmp_files.append(mdout)
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
# Unzip topology to topology_out
top_file = fu.unzip_top(zip_file=self.input_top_zip_path,
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
if self.input_mdp_path:
self.output_mdp_path = self.input_mdp_path
else:
mdp_dir = fu.create_unique_dir()
tmp_files.append(mdp_dir)
self.output_mdp_path = self.create_mdp(
path=str(Path(mdp_dir).joinpath(self.output_mdp_path)))
md = self.mdp.get('type', 'minimization')
if md not in ('index', 'free'):
fu.log('Will run a %s md of %s steps' % (md, self.nsteps), out_log,
self.global_log)
elif md == 'index':
fu.log('Will create a TPR to be used as structure file')
else:
fu.log(
'Will run a %s md of %s' %
(md, fu.human_readable_time(
int(self.nsteps) * float(self.dt))), out_log,
self.global_log)
if self.container_path:
fu.log('Container execution enabled', out_log)
shutil.copy2(self.output_mdp_path,
container_io_dict.get("unique_dir"))
self.output_mdp_path = str(
Path(self.container_volume_path).joinpath(
Path(self.output_mdp_path).name))
shutil.copytree(
top_dir,
str(
Path(container_io_dict.get("unique_dir")).joinpath(
Path(top_dir).name)))
top_file = str(
Path(self.container_volume_path).joinpath(
Path(top_dir).name,
Path(top_file).name))
cmd = [
self.gmx_path, 'grompp', '-f', self.output_mdp_path, '-c',
container_io_dict["in"]["input_gro_path"], '-r',
container_io_dict["in"]["input_gro_path"], '-p', top_file, '-o',
container_io_dict["out"]["output_tpr_path"], '-po', mdout,
'-maxwarn', self.maxwarn
]
if container_io_dict["in"].get("input_cpt_path") and Path(
container_io_dict["in"]["input_cpt_path"]).exists():
cmd.append('-t')
if self.container_path:
shutil.copy2(container_io_dict["in"]["input_cpt_path"],
container_io_dict.get("unique_dir"))
cmd.append(
str(
Path(self.container_volume_path).joinpath(
Path(container_io_dict["in"]
["input_cpt_path"]).name)))
else:
cmd.append(container_io_dict["in"]["input_cpt_path"])
if container_io_dict["in"].get("input_ndx_path") and Path(
container_io_dict["in"]["input_ndx_path"]).exists():
cmd.append('-n')
if self.container_path:
shutil.copy2(container_io_dict["in"]["input_ndx_path"],
container_io_dict.get("unique_dir"))
cmd.append(
Path(self.container_volume_path).joinpath(
Path(container_io_dict["in"]["input_ndx_path"]).name))
else:
cmd.append(container_io_dict["in"]["input_ndx_path"])
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS editconf module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if not self.container_path:
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'editconf', '-f',
container_io_dict["in"]["input_gro_path"], '-o',
container_io_dict["out"]["output_gro_path"], '-d',
str(self.distance_to_molecule), '-bt', self.box_type
]
if self.center_molecule:
cmd.append('-c')
fu.log('Centering molecule in the box.', out_log, self.global_log)
fu.log(
"Distance of the box to molecule: %6.2f" %
self.distance_to_molecule, out_log, self.global_log)
fu.log("Box type: %s" % self.box_type, out_log, self.global_log)
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode
def launch(self) -> int:
"""Launches the execution of the GROMACS mdrun module."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Check GROMACS version
if (not self.mpi_bin) and (not self.container_path):
if self.gmx_version < 512:
raise GromacsVersionError(
"Gromacs version should be 5.1.2 or newer %d detected" %
self.gmx_version)
fu.log(
"GROMACS %s %d version detected" %
(self.__class__.__name__, self.gmx_version), out_log)
# Restart if needed
if self.restart:
if fu.check_complete_files(self.io_dict["out"].values()):
fu.log(
'Restart is enabled, this step: %s will the skipped' %
self.step, out_log, self.global_log)
return 0
container_io_dict = fu.copy_to_container(self.container_path,
self.container_volume_path,
self.io_dict)
cmd = [
self.gmx_path, 'mdrun', '-s',
container_io_dict["in"]["input_tpr_path"], '-o',
container_io_dict["out"]["output_trr_path"], '-c',
container_io_dict["out"]["output_gro_path"], '-e',
container_io_dict["out"]["output_edr_path"], '-g',
container_io_dict["out"]["output_log_path"], '-nt',
self.num_threads
]
if self.use_gpu:
cmd += ["-nb", "gpu", "-pme", "gpu"]
if self.mpi_bin:
mpi_cmd = [self.mpi_bin]
if self.mpi_np:
mpi_cmd.append('-np')
mpi_cmd.append(str(self.mpi_np))
if self.mpi_hostlist:
mpi_cmd.append('-hostfile')
mpi_cmd.append(self.mpi_hostlist)
cmd = mpi_cmd + cmd
if container_io_dict["out"].get("output_xtc_path"):
cmd.append('-x')
cmd.append(container_io_dict["out"]["output_xtc_path"])
if container_io_dict["out"].get("output_cpt_path"):
cmd.append('-cpo')
cmd.append(container_io_dict["out"]["output_cpt_path"])
if container_io_dict["out"].get("output_dhdl_path"):
cmd.append('-dhdl')
cmd.append(container_io_dict["out"]["output_dhdl_path"])
new_env = None
if self.gmxlib:
new_env = os.environ.copy()
new_env['GMXLIB'] = self.gmxlib
cmd = fu.create_cmd_line(
cmd,
container_path=self.container_path,
host_volume=container_io_dict.get("unique_dir"),
container_volume=self.container_volume_path,
container_working_dir=self.container_working_dir,
container_user_uid=self.container_user_id,
container_shell_path=self.container_shell_path,
container_image=self.container_image,
out_log=out_log,
global_log=self.global_log)
returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log,
self.global_log, new_env).launch()
fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)
tmp_files.append(container_io_dict.get("unique_dir"))
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return returncode