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)
# Restart if needed
if self.restart:
output_file_list = [self.io_dict['out'].get("output_top_zip_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
# Unzip topology
top_file = fu.unzip_top(
zip_file=self.io_dict['in'].get("input_top_zip_path"),
out_log=out_log)
top_dir = str(Path(top_file).parent)
tmp_files.append(top_dir)
itp_name = str(Path(self.io_dict['in'].get("input_itp_path")).name)
with open(top_file) as top_f:
top_lines = top_f.readlines()
top_f.close()
fu.rm(top_file)
forcefield_pattern = r'#include.*forcefield.itp\"'
for index, line in enumerate(top_lines):
if re.search(forcefield_pattern, line):
break
top_lines.insert(index + 1, '\n')
top_lines.insert(index + 2, '; Including ligand ITP\n')
top_lines.insert(index + 3, '#include "' + itp_name + '"\n')
top_lines.insert(index + 4, '\n')
if self.io_dict['in'].get("input_posres_itp_path"):
top_lines.insert(index + 5, '; Ligand position restraints' + '\n')
top_lines.insert(index + 6, '#ifdef ' + self.posres_name + '\n')
top_lines.insert(
index + 7, '#include "' + str(
Path(self.io_dict['in'].get("input_posres_itp_path")).name)
+ '"\n')
top_lines.insert(index + 8, '#endif' + '\n')
top_lines.insert(index + 9, '\n')
inside_moleculetype_section = False
with open(self.io_dict['in'].get("input_itp_path")) as itp_file:
moleculetype_pattern = r'\[ moleculetype \]'
for line in itp_file:
if re.search(moleculetype_pattern, line):
inside_moleculetype_section = True
continue
if inside_moleculetype_section and not line.startswith(';'):
moleculetype = line.strip().split()[0].strip()
break
molecules_pattern = r'\[ molecules \]'
inside_molecules_section = False
index_molecule = None
molecule_string = moleculetype + (20 -
len(moleculetype)) * ' ' + '1' + '\n'
for index, line in enumerate(top_lines):
if re.search(molecules_pattern, line):
inside_molecules_section = True
continue
if inside_molecules_section and not line.startswith(
';') and line.upper().startswith('PROTEIN'):
index_molecule = index
if index_molecule:
top_lines.insert(index_molecule + 1, molecule_string)
else:
top_lines.append(molecule_string)
new_top = fu.create_name(path=top_dir,
prefix=self.prefix,
step=self.step,
name='ligand.top')
with open(new_top, 'w') as new_top_f:
new_top_f.write("".join(top_lines))
shutil.copy2(self.io_dict['in'].get("input_itp_path"), top_dir)
if self.io_dict['in'].get("input_posres_itp_path"):
shutil.copy2(self.io_dict['in'].get("input_posres_itp_path"),
top_dir)
# zip topology
fu.log(
'Compressing topology to: %s' %
self.io_dict['out'].get("output_top_zip_path"), out_log,
self.global_log)
fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path"),
top_file=new_top,
out_log=out_log)
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return 0
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) -> int:
"""Launch the topology generation."""
tmp_files = []
# Get local loggers from launchlogger decorator
out_log = getattr(self, 'out_log', None)
err_log = getattr(self, 'err_log', None)
# Restart if needed
if self.restart:
output_file_list = [self.io_dict['out'].get("output_top_zip_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
top_file = fu.unzip_top(zip_file=self.io_dict['in'].get("input_top_zip_path"), out_log=out_log)
# Create index list of index file :)
index_dic = {}
lines = open(self.io_dict['in'].get("input_ndx_path")).read().splitlines()
for index, line in enumerate(lines):
if line.startswith('['):
index_dic[line] = index,
label = line
if index > 0:
index_dic[label] = index_dic[label][0], index
index_dic[label] = index_dic[label][0], index
fu.log('Index_dic: '+str(index_dic), out_log, self.global_log)
self.ref_rest_chain_triplet_list = [tuple(elem.strip(' ()').replace(' ', '').split(',')) for elem in self.ref_rest_chain_triplet_list.split('),')]
fu.log('ref_rest_chain_triplet_list: ' + str(self.ref_rest_chain_triplet_list), out_log, self.global_log)
for reference_group, restrain_group, chain in self.ref_rest_chain_triplet_list:
fu.log('Reference group: '+reference_group, out_log, self.global_log)
fu.log('Restrain group: '+restrain_group, out_log, self.global_log)
fu.log('Chain: '+chain, out_log, self.global_log)
self.io_dict['out']["output_itp_path"] = fu.create_name(path=str(Path(top_file).parent), prefix=self.prefix, step=self.step, name=restrain_group+'.itp')
# Mapping atoms from absolute enumeration to Chain relative enumeration
fu.log('reference_group_index: start_closed:'+str(index_dic['[ '+reference_group+' ]'][0]+1)+' stop_open: '+str(index_dic['[ '+reference_group+' ]'][1]), out_log, self.global_log)
reference_group_list = [int(elem) for line in lines[index_dic['[ '+reference_group+' ]'][0]+1: index_dic['[ '+reference_group+' ]'][1]] for elem in line.split()]
fu.log('restrain_group_index: start_closed:'+str(index_dic['[ '+restrain_group+' ]'][0]+1)+' stop_open: '+str(index_dic['[ '+restrain_group+' ]'][1]), out_log, self.global_log)
restrain_group_list = [int(elem) for line in lines[index_dic['[ '+restrain_group+' ]'][0]+1: index_dic['[ '+restrain_group+' ]'][1]] for elem in line.split()]
selected_list = [reference_group_list.index(atom)+1 for atom in restrain_group_list]
# Creating new ITP with restrictions
with open(self.io_dict['out'].get("output_itp_path"), 'w') as f:
fu.log('Creating: '+str(f)+' and adding the selected atoms force constants', out_log, self.global_log)
f.write('[ position_restraints ]\n')
f.write('; atom type fx fy fz\n')
for atom in selected_list:
f.write(str(atom)+' 1 '+self.force_constants+'\n')
# Including new ITP in the corresponding ITP-chain file
for file_dir in Path(top_file).parent.iterdir():
if not file_dir.name.startswith("posre") and not file_dir.name.endswith("_pr.itp"):
if fnmatch.fnmatch(str(file_dir), "*_chain_"+chain+".itp"):
with open(str(file_dir), 'a') as f:
fu.log('Opening: '+str(f)+' and adding the ifdef include statement', out_log, self.global_log)
f.write('\n')
f.write('; Include Position restraint file\n')
f.write('#ifdef CUSTOM_POSRES\n')
f.write('#include "'+str(Path(self.io_dict['out'].get("output_itp_path")).name)+'"\n')
f.write('#endif\n')
# zip topology
fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path"), top_file=top_file, out_log=out_log)
if self.remove_tmp:
fu.rm_file_list(tmp_files, out_log=out_log)
return 0
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